a ggplot on which you want to add summary statistics.

a function that is given the complete data and should return a data frame with variables ymin, y, and ymax. Allowed values are one of: "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range".

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange".

point or outline color.

fill color. Used only whne error.plot = "crossbar".

grouping variable. Allowed values are 1 (for one group) or a character vector specifying the name of the grouping variable. Used only for adding statistical summary per group.

numeric value between 0 and 1 specifying bar or box width. Example width = 0.8. Used only when error.plot is one of c("crossbar", "errorbar").

point shape. Allowed values can be displayed using the function show_point_shapes().

numeric value in [0-1] specifying point and line size.

line type.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

the percent range of the confidence interval (default is 0.95).

a data.frame to be displayed. If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot.

position adjustment, either as a string, or the result of a call to a position adjustment function. Used to adjust position for multiple groups.

a numeric vector.

allowed values are one of ("both", "lower", "upper", "none") specifying whether to plot the lower and/or the upper limits of error interval.

(arranged) ggplots.

optional string, or grob.

figure label (e.g.: "Figure 1").

position of the figure label, can be one of "top.left", "top", "top.right", "bottom.left", "bottom", "bottom.right". Default is "top.left".

optional size of the figure label.

optional font face of the figure label. Allowed values include: "plain", "bold", "italic", "bold.italic".

an object of class gtable or grob as returned by the functions arrangeGrob() and grid.arrange().

numeric (in [0-1]) or character vector of coordinates. If character, should be one of c('right', 'left', 'bottom', 'top', 'center', 'centre', 'middle').

integer ggplot's group id. Used to shift coordinates to avoid overlaps.

numeric value in [0-1]. The step size for shifting coordinates in npc units. Considered as horizontal step for x-axis and vertical step for y-axis. For y-axis, the step value can be negative to reverse the order of groups.

numeric [0-1] The margin added towards the nearest plotting area edge when converting character coordinates into npc.

the concerned axis . Should be one of c("xy", "x", "y").

axis scale. Allowed values are one of c("none", "log2", "log10", "sqrt", "percent", "dollar", "scientific"); e.g.: .scale="log2".

ogical value. If TRUE, axis tick mark labels will be formatted when .scale = "log2" or "log10".

raster object to display, as returned by the function readPNG()[in png package] and readJPEG() [in jpeg package].

background color.

border line color.

numeric value specifying border line size.

line type. An integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, twodash). Sess show_line_types.

a formula of the form x ~ group where x is a numeric variable giving the data values and group is a factor with one or multiple levels giving the corresponding groups. For example, formula = TP53 ~ cancer_group.

It's also possible to perform the test for multiple response variables at the same time. For example, formula = c(TP53, PTEN) ~ cancer_group.

a data.frame containing the variables in the formula.

the type of test. Default is wilcox.test. Allowed values include:

• t.test (parametric) and wilcox.test (non-parametric). Perform comparison between two groups of samples. If the grouping variable contains more than two levels, then a pairwise comparison is performed.

• anova (parametric) and kruskal.test (non-parametric). Perform one-way ANOVA test comparing multiple groups.

a logical indicating whether you want a paired test. Used only in t.test and in wilcox.test.

a character vector containing the name of grouping variables.

a character string specifying the reference group. If specified, for a given grouping variable, each of the group levels will be compared to the reference group (i.e. control group).

ref.group can be also ".all.". In this case, each of the grouping variable levels is compared to all (i.e. basemean).

a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

method for adjusting p values (see p.adjust). Has impact only in a situation, where multiple pairwise tests are performed; or when there are multiple grouping variables. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".

Note that, when the formula contains multiple variables, the p-value adjustment is done independently for each variable.

Other arguments to be passed to the test function.

a list of aesthetic arguments; for example .list = list(x = "dose", y = "len", color = "dose").

logical. If TRUE, parse the input as an expression.

a data frame.

the name of a column containing the variable to be summarized.

a character vector containing grouping variables; e.g.: grps = c("grp1", "grp2")

the percent range of the confidence interval (default is 0.95).

a ggplot

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

Number of rows and columns in the panel. Used only when the data is faceted by one grouping variable.

should axis scales of panels be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y").

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

Character vector. An alternative to the argument short.panel.labs. Possible values are one of "label_both" (panel labelled by both grouping variable names and levels) and "label_value" (panel labelled with only grouping levels).

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

a list to customize the background of panel labels. Should contain the combination of the following elements:

• color, linetype, size: background line color, type and size

• fill: background fill color.

For example, panel.labs.background = list(color = "blue", fill = "pink", linetype = "dashed", size = 0.5).

a list of aestheics indicating the size (e.g.: 14), the face/style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") and the orientation angle (e.g.: 45) of panel labels.

same as panel.labs.font but for only x and y direction, respectively.

(used only in facet_wrap()). By default, the labels are displayed on the top of the plot. Using strip.position it is possible to place the labels on either of the four sides by setting strip.position = c("top", "bottom", "left", "right")

not used

character string specifying the plot components. Allowed values include:

• "title" for the main title

• "subtitle" for the plot subtitle

• "caption" for the plot caption

• "legend.title" for the legend title

• "legend.text" for the legend text

• "x", "xlab", or "x.title" for x axis label

• "y", "ylab", or "y.title" for y axis label

• "xy", "xylab", "xy.title" or "axis.title" for both x and y axis labels

• "x.text" for x axis texts (x axis tick labels)

• "y.text" for y axis texts (y axis tick labels)

• "xy.text" or "axis.text" for both x and y axis texts

numeric value specifying the font size, (e.g.: size = 12).

character string specifying the font color, (e.g.: color = "red").

the font face or style. Allowed values include one of "plain", "bold", "italic", "bold.italic", (e.g.: face = "bold.italic").

the font family.

other arguments to pass to the function element_text().

a ggplot2 function (e.g.: geom_point)

a data frame to be used for mapping

Position adjustment, either as a string, or the result of a call to a position adjustment function.

arguments accepted by the function

number of breaks.

number: the step between breaks.

the starting value of breaks. By default, 0 is used for positive variables

the end values of breaks. This corresponds generally to the maximum limit of the axis.

integer ggplot's group id. Used to shift coordinates to avoid overlaps.

a numeric vector of length 2 containing the data ranges (minimum and the maximum). Should be specified only when coord = NULL and npc is specified. Used to convert npc to data coordinates. Considered only when the argument npc is specified.

data coordinates (i.e., either x or y coordinates).

numeric (in [0-1]) or character vector of coordinates. If character, should be one of c('right', 'left', 'bottom', 'top', 'center', 'centre', 'middle'). Note that, the data.ranges, step and margin.npc, arguments are considered only when npc is specified. The option npc is ignored when the argument coord is specified.

numeric value in [0-1]. The step size for shifting coordinates in npc units. Considered as horizontal step for x-axis and vertical step for y-axis. For y-axis, the step value can be negative to reverse the order of groups.

numeric [0-1] The margin added towards the nearest plotting area edge when converting character coordinates into npc.

an object of class ggplot or a list of ggplots. If p is a list, only the first legend is returned.

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none".

Color palette. Allowed values include:

• Grey color palettes: "grey" or "gray";

• RColorBrewer palettes, see brewer.pal and details section. Examples of palette names include: "RdBu", "Blues", "Dark2", "Set2", ...;

• Custom color palettes. For example, palette = c("#00AFBB", "#E7B800", "#FC4E07");

• ggsci scientific journal palettes, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

the number of colors to generate.

a ggplot

character vector specifying other plot elements to be added. Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range".

point or outline color.

fill color. Used only when error.plot = "crossbar".

grouping variable. Allowed values are 1 (for one group) or a character vector specifying the name of the grouping variable. Used only for adding statistical summary per group.

numeric value between 0 and 1 specifying bar or box width. Example width = 0.8. Used only when error.plot is one of c("crossbar", "errorbar").

point shape. Allowed values can be displayed using the function show_point_shapes().

numeric value in [0-1] specifying point and line size.

numeric value specifying fill color transparency. Value should be in [0, 1], where 0 is full transparency and 1 is no transparency.

a numeric value specifying the amount of jittering. Used only when add contains "jitter".

A random seed to make the jitter reproducible. Default is '123'. Useful if you need to apply the same jitter twice, e.g., for a point and a corresponding label. The random seed is reset after jittering. If 'NA', the seed is initialized with a random value; this makes sure that two subsequent calls start with a different seed. Use NULL to use the current random seed and also avoid resetting (the behaviour of ggplot 2.2.1 and earlier).

numeric value specifying bin width. use value between 0 and 1 when you have a strong dense dotplot. For example binwidth = 0.2. Used only when add contains "dotplot".

as size but applied only to dotplot.

line type.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange".

the percent range of the confidence interval (default is 0.95).

a data.frame to be displayed. If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot.

position adjustment, either as a string, or the result of a call to a position adjustment function. Used to adjust position for multiple groups.

the geometry of the main plot. Ex: p_geom = "geom_line". If NULL, the geometry is extracted from p. Used only by ggline().

a ggplot

An integer indicating the statistical layer rank in the ggplot (in the order added to the plot).

method for adjusting p values (see p.adjust). Has impact only in a situation, where multiple pairwise tests are performed; or when there are multiple grouping variables. Ignored when the specified method is "tukey_hsd" or "games_howell_test" because they come with internal p adjustment method. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".

character string specifying label. Can be:

• the column containing the label (e.g.: label = "p" or label = "p.adj"), where p is the p-value. Other possible values are "p.signif", "p.adj.signif", "p.format", "p.adj.format".

• an expression that can be formatted by the glue() package. For example, when specifying label = "Wilcoxon, p = \{p\}", the expression {p} will be replaced by its value.

• a combination of plotmath expressions and glue expressions. You may want some of the statistical parameter in italic; for example:label = "Wilcoxon, italic(p)= {p}"

.

can be logical value (TRUE or FALSE) or a character vector ("p.adj" or "p").

a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

character. Possible values are one of c("plot", "stat_test"). Default is "plot".

list of plots to be arranged into the grid. The plots can be either ggplot2 plot objects or arbitrary gtables.

(optional) list of plots to display.

(optional) number of columns in the plot grid.

(optional) number of rows in the plot grid.

(optional) list of labels to be added to the plots. You can also set labels="AUTO" to auto-generate upper-case labels or labels="auto" to auto-generate lower-case labels.

(optional) Single value or vector of x positions for plot labels, relative to each subplot. Defaults to 0 for all labels. (Each label is placed all the way to the left of each plot.)

(optional) Single value or vector of y positions for plot labels, relative to each subplot. Defaults to 1 for all labels. (Each label is placed all the way to the top of each plot.)

Adjusts the horizontal position of each label. More negative values move the label further to the right on the plot canvas. Can be a single value (applied to all labels) or a vector of values (one for each label). Default is -0.5.

Adjusts the vertical position of each label. More positive values move the label further down on the plot canvas. Can be a single value (applied to all labels) or a vector of values (one for each label). Default is 1.5.

a list of arguments for customizing labels. Allowed values are the combination of the following elements: size (e.g.: 14), face (e.g.: "plain", "bold", "italic", "bold.italic"), color (e.g.: "red") and family. For example font.label = list(size = 14, face = "bold", color ="red").

(optional) Specifies whether graphs in the grid should be horizontally ("h") or vertically ("v") aligned. Options are "none" (default), "hv" (align in both directions), "h", and "v".

(optional) numerical vector of relative columns widths. For example, in a two-column grid, widths = c(2, 1) would make the first column twice as wide as the second column.

same as widths but for column heights.

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none".

logical value. Default is FALSE. If TRUE, a common unique legend will be created for arranged plots.

a legend grob as returned by the function get_legend(). If provided, it will be used as the common legend.

a data frame. Can be:

• a standard contingency table formed by two categorical variables: a data frame with row names and column names. The categories of the first variable are columns and the categories of the second variable are rows.

• a streched contingency table: a data frame containing at least three columns corresponding, respectively, to (1) the categories of the first variable, (2) the categories of the second varible, (3) the frequency value. In this case, you should specify the argument x and y in the function ggballoonplot()

.

the column names specifying, respectively, the first and the second variable forming the contingency table. Required only when the data is a stretched contingency table.

point size. By default, the points size reflects the relative magnitude of the value of the corresponding cell (size = "value"). Can be also numeric (size = 4).

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a numeric vector of length 2 that specifies the minimum and maximum size of the plotting symbol. Default values are size.range = c(1, 10).

points shape. The default value is 21. Alternaive values include 22, 23, 24, 25.

point border line color.

point fill color. Default is "lightgray". Considered only for points 21 to 25.

logical. If TRUE, show the data cell values as point labels.

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of point labels. For example font.label = c(14, "bold", "red"). To specify only the size and the style, use font.label = c(14, "plain").

logica. If TRUE (default), rotate the x axis text.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments passed to the function ggpar

a data frame

x and y variables for drawing.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline and fill colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

numeric value between 0 and 1 specifying box width.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

specify whether to add labels on the bar plot. Allowed values are:

• logical value: If TRUE, y values is added as labels on the bar plot

• character vector: Used as text labels; must be the same length as y.

text color and size for labels.

character specifying the position for labels. Allowed values are "out" (for outside) or "in" (for inside). Ignored when lab.vjust != NULL.

numeric, vertical justification of labels. Provide negative value (e.g.: -0.4) to put labels outside the bars or positive value to put labels inside (e.g.: 2).

numeric, horizontal justification of labels.

integer indicating the number of decimal places (round) to be used.

a string specifying whether the value should be sorted. Allowed values are "none" (no sorting), "asc" (for ascending) or "desc" (for descending).

logical value. If TRUE the data are sorted by groups. Used only when sort.val != "none".

a numeric value specifying the number of top elements to be shown.

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to be passed to ggpar().

a data frame

character string containing the name of x variable.

character vector containing one or more variables to plot

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline color.

fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

logical value. If TRUE, shows error bars of box plots.

numeric value specifying the width of box plot error bars. Default is 0.4.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

line types.

Numeric value (e.g.: size = 1). change the size of points and outlines.

numeric value between 0 and 1 specifying box width.

If FALSE (default) make a standard box plot. If TRUE, make a notched box plot. Notches are used to compare groups; if the notches of two boxes do not overlap, this suggests that the medians are significantly different.

point shape of outlier. Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_boxplot, ggpar and facet.

a data frame

variable to be drawn.

one of "density" or "count".

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

density line color and fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

line type. See show_line_types.

numeric value specifying fill color transparency. Value should be in [0, 1], where 0 is full transparency and 1 is no transparency.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

allowed values are one of "mean" or "median" (for adding mean or median line, respectively).

parameters (color, size, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

logical value. If TRUE, add marginal rug.

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_density and ggpar.

a data frame

variable containing values for drawing.

variable specifying the label of each slice.

character specifying the position for labels. Allowed values are "out" (for outside) or "in" (for inside).

numeric value, used to adjust label position when lab.pos = "in". Increase or decrease this value to see the effect.

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of label font. For example lab.font= c(4, "bold", "red").

character vector specifying font family.

outline and fill colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to be passed to ggpar().

a data frame

x and y variables for drawing.

an optional column name indicating how the elements of x are grouped.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

points color and size.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

point shape. See show_point_shapes.

numeric value specifying the dot size.

a character vector for sorting into ascending or descending order. Allowed values are one of "descending", "ascending" and "none". Partial match are allowed (e.g. sorting = "desc" or "asc"). Default is "descending".

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

logical. If TRUE (default), x axis texts are colored by groups.

logical value. If TRUE, rotate the graph by setting the plot orientation to horizontal.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

the name of the column containing point labels.

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

Position adjustment, either as a string, or the result of a call to a position adjustment function.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_point and ggpar.

a data frame

character string containing the name of x variable.

character vector containing one or more variables to plot

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline color.

fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

Numeric value (e.g.: size = 1). change the size of points and outlines.

numeric value specifying bin width. use value between 0 and 1 when you have a strong dense dotplot. For example binwidth = 0.2.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_dotplot, ggpar and facet.

a data frame

variable to be drawn.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

line and point color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

line and point size.

line type. See show_line_types.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to stat_ecdf and ggpar.

a data frame

x and y variables for drawing.

descriptive statistics to be used for visualizing errors. Default value is "mean_se". Allowed values are one of , "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see desc_statby for more details.

logical. If TRUE, x axis will be treated as numeric. Default is FALSE.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline and fill colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

numeric value between 0 and 1 specifying box width.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items. Considered only when x axis is a factor variable.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the percent range of the confidence interval (default is 0.95).

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to be passed to ggpar().

list of plots to be arranged into the grid. The plots can be either ggplot2 plot objects, arbitrary gtables or an object of class ggarrange.

(optional) list of plots to display.

File name to create on disk.

(optional) number of columns in the plot grid.

(optional) number of rows in the plot grid.

plot width and height, respectively (example, width = 800, height = 800). Applied only to raster plots: "png", "jpeg", "jpg", "bmp" and "tiff".

the default pointsize of plotted text (example, pointsize = 8). Used only for raster plots.

the resolution in ppi (example, res = 250). Used only for raster plots.

logical. If TRUE, show message.

a data frame

variable to be drawn.

one of "density" or "count".

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

a variable name available in the input data for creating a weighted histogram.

histogram line color and fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

line type. See show_line_types.

numeric value specifying fill color transparency. Value should be in [0, 1], where 0 is full transparency and 1 is no transparency.

Number of bins. Defaults to 30.

numeric value specifying bin width. use value between 0 and 1 when you have a strong dense dotplot. For example binwidth = 0.2.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

allowed values are one of "mean" or "median" (for adding mean or median line, respectively).

parameters (color, size, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

logical value. If TRUE, add marginal rug.

logical value. If TRUE, add density curves.

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

Position adjustment, either as a string, or the result of a call to a position adjustment function. Allowed values include "identity", "stack", "dodge".

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_histogram and ggpar.

a data frame

x and y variables for drawing.

grouping variable to connect points by line. Allowed values are 1 (for one line, one group) or a character vector specifying the name of the grouping variable (case of multiple lines).

logical. If TRUE, x axis will be treated as numeric. Default is FALSE.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

line colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

line type.

plot type. Allowed values are one of "b" for both line and point; "l" for line only; and "p" for point only. Default is "b".

Numeric value (e.g.: size = 1). change the size of points and outlines.

point shapes.

point stroke. Used only for shapes 21-24 to control the thickness of points border.

point size.

point color.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

logical value. If TRUE, shows line labels.

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_dotplot.

an object of class DESeqResults, get_diff, DE_Results, matrix or data frame containing the columns baseMean (or baseMeanLog2), log2FoldChange, and padj. Rows are genes.

Two possible formats are accepted for the input data:

• 1/ baseMean | log2FoldChange | padj. This is a typical output from DESeq2 pipeline. Here, we'll use log2(baseMean) as the x-axis variable.

• 2/ baseMeanLog2 | log2FoldChange | padj. Here, baseMeanLog2 is assumed to be the mean of logged values; so we'll use it as the x-axis variable without any transformation. This is the real A in MA plot. In other words, it is the average of two log-scales values: A = (log2(x) + log2(y))/2 = log2(xy)*1/2

Terminology:

• baseMean: the mean expression of genes in the two groups.

• log2FoldChange: the log2 fold changes of group 2 compared to group 1

• padj: the adjusted p-value of the used statiscal test.

Accepted false discovery rate for considering genes as differentially expressed.

the fold change threshold. Only genes with a fold change >= fc and padj <= fdr are considered as significantly differentially expressed.

a character vector of length nrow(data) specifying gene names corresponding to each row. Used for point labels.

a numeric vector with length = nrow(data), specifying if the genes is expressed (value = 1) or not (value = 0). For example detection_call = c(1, 1, 0, 1, 0, 1). Default is NULL. If detection_call column is available in data, it will be used.

points size.

numeric value betwenn 0 an 1 specifying point alpha for controlling transparency. For example, use alpha = 0.5.

Random seed passed to set.seed. if NA, set.seed will not be called. Default is 42 for reproducibility.

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of point labels. For example font.label = c(14, "bold", "red").

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

the number of top genes to be shown on the plot. Use top = 0 to hide to gene labels.

methods to be used for selecting top genes. Allowed values include "padj" and "fc" for selecting by adjusted p values or fold changes, respectively.

character vector specifying some labels to show.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to ggpar.

a data frame

variable name corresponding to the first condition.

variable name corresponding to the second condition.

x and y variables, where x is a grouping variable and y contains values for each group. Considered only when cond1 and cond2 are missing.

variable name corresponding to paired samples' id. Used to connect paired points with lines.

points and box plot colors. To color by conditions, use color = "condition".

box plot fill color. To change fill color by conditions, use fill = "condition".

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

box plot width.

point and line size, respectively.

line color.

line type.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to be passed to ggpar().

an object of class ggplot or a list of ggplots

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". Can be also a numeric vector of length(groups); in this case a basic color palette is created using the function palette.

vector of colors to use for n-colour gradient. Allowed values include brewer and ggsci color palettes.

plot main title.

plot subtitle.

plot caption.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

plot main title.

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of main title, subtitle, caption, xlab and ylab, respectively. For example font.x = c(14, "bold", "red"). Use font.x = 14, to change only font size; or use font.x = "bold", to change only font face.

alias of font.submain and font.submain, respectively.

character vector specifying font family.

a numeric vector of length 2, specifying x and y axis limits (minimum and maximum), respectively. e.g.: ylim = c(0, 50).

x and y axis scale, respectively. Allowed values are one of c("none", "log2", "log10", "sqrt"); e.g.: yscale="log2".

logical value. If TRUE, axis tick mark labels will be formatted when xscale or yscale = "log2" or "log10".

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); see details section.

legend title, e.g.: legend.title = "Species". Can be also a list, legend.title = list(color = "Species", linetype = "Species", shape = "Species").

legend text font style; e.g.: font.legend = c(10, "plain", "black").

logical value. Default is TRUE. If FALSE, hide axis tick marks.

logical value. Default is TRUE. If FALSE, hide axis tick labels.

Font style (size, face, color) for tick labels, e.g.: c(14, "bold", "red").

Numeric value specifying the rotation angle of x and y axis tick labels, respectively. Default value is NULL. For vertical x axis texts use x.text.angle = 90.

Same as x.text.angle and y.text.angle, respectively. Will be deprecated in the near future.

numeric value controlling x and y axis breaks, respectively. For example, if yticks.by = 5, a tick mark is shown on every 5. Default value is NULL.

logical value. If TRUE, rotate the graph by setting the plot orientation to horizontal.

change the orientation of the plot. Allowed values are one of c( "vertical", "horizontal", "reverse"). Partial match is allowed.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

not used

the text to plot.

font color, example: color = "black"

font size, example: size = 12

font face. Allowed values are one of "plain", "italic", "bold", "bold.italic".

font family

Line height, example: lineheight = 2.

a grid grob

a logical value indicating whether a grob is being added to the display list or redrawn from the display list.

a data frame

variable containing values for drawing.

variable specifying the label of each slice.

character specifying the position for labels. Allowed values are "out" (for outside) or "in" (for inside).

numeric value, used to adjust label position when lab.pos = "in". Increase or decrease this value to see the effect.

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of label font. For example lab.font= c(4, "bold", "red").

character vector specifying font family.

outline and fill colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

Numeric value (e.g.: size = 1). change the size of points and outlines.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to be passed to ggpar().

a data frame

character string containing the name of x variable.

character vector containing one or more variables to plot

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline color.

fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

line types.

Numeric value (e.g.: size = 1). change the size of points and outlines.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

a data frame

variable to be drawn.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

point color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

point size.

point shape.

character vector. Allowed values are one of "none" and "qqline" (for adding qqline).

parameters (color, size, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

logical value. If TRUE, confidence interval is added.

the confidence level. Default value is 0.95.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to ggpar.

a data frame

x variables for drawing.

y variables for drawing.

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

point colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

point shape. See show_point_shapes.

Numeric value (e.g.: size = 1). change the size of points and outlines.

logical value. If TRUE, show points.

logical value. If TRUE, add marginal rug.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

allowed values are one of "none", "reg.line" (for adding linear regression line) or "loess" (for adding local regression fitting).

parameters (color, size, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

logical value. If TRUE, adds confidence interval.

Level controlling confidence region. Default is 95%. Used only when add != "none" and conf.int = TRUE.

should the fit span the full range of the plot, or just the data. Used only when add != "none".

logical value. If TRUE, draws ellipses around points.

the size of the concentration ellipse in normal probability.

Character specifying frame type. Possible values are "convex", "confidence" or types supported by stat_ellipse() including one of c("t", "norm", "euclid") for plotting concentration ellipses.

• "convex": plot convex hull of a set o points.

• "confidence": plot confidence ellipses arround group mean points as FactoMineR::coord.ellipse().

• "t": assumes a multivariate t-distribution.

• "norm": assumes a multivariate normal distribution.

• "euclid": draws a circle with the radius equal to level, representing the euclidean distance from the center. This ellipse probably won't appear circular unless coord_fixed() is applied.

Alpha for ellipse specifying the transparency level of fill color. Use alpha = 0 for no fill color.

logical value. If TRUE, remove ellipse border lines.

logical value. If TRUE, group mean points are added to the plot.

numeric value specifying the size of mean points.

logical value. If TRUE, a star plot is generated.

line type and line width (size) for star plot, respectively.

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of point labels. For example font.label = c(14, "bold", "red"). To specify only the size and the style, use font.label = c(14, "plain").

character vector specifying font family.

character vector specifying some labels to show.

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

logical value. If TRUE, correlation coefficient with the p-value will be added to the plot.

a list of arguments to pass to the function stat_cor for customizing the displayed correlation coefficients. For example: cor.coeff.args = list(method = "pearson", label.x.npc = "right", label.y.npc = "top").

method for computing correlation coefficient. Allowed values are one of "pearson", "kendall", or "spearman".

numeric vector, of length 2, specifying the x and y coordinates of the correlation coefficient. Default values are NULL.

correlation coefficient text font size.

a ggplot. If not NULL, points are added to an existing plot.

logical. Should text be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_point and ggpar.

a data frame

an object of class ggscatterhist.

y variables for drawing.

a grouping variable. Change points color and shape by groups if the options color and shape are missing. Should be also specified when you want to create a marginal box plot that is grouped.

point colors.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

point shape. See show_point_shapes.

Numeric value (e.g.: size = 1). change the size of points and outlines.

line type ("solid", "dashed", ...)

Number of histogram bins. Defaults to 30. Pick a better value that fit to your data.

the type of the marginal plot. Default is "hist".

parameters to be applied to the marginal plots.

the theme of the marginal plot. Default is theme_void().

logical value. If TRUE, adds space between the main plot and the marginal plot.

the width of the main plot. Default is 2.

the width of the marginal plot. Default is 1.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

specify the legend position. Allowed values include: "top", "bottom", "left", "right".

the theme to be used for the scatter plot. Default is theme_pubr().

logical value. If TRUE (default), print the plot.

other arguments passed to the function ggscatter().

a data frame

character string containing the name of x variable.

character vector containing one or more variables to plot

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline color.

fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

point shape

Numeric value (e.g.: size = 1). change the size of points and outlines.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

the amount of jitter.

position adjustment, either as a string, or the result of a call to a position adjustment function. Used to adjust position for multiple groups.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_jitter, ggpar and facet.

a data frame

a list of ggsummarystats.

character vector containing one or more variables to plot

integer indicating the number of decimal places (round) to be used.

Numeric value (e.g.: size = 1). change the size of points and outlines.

outline color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

Character vector. An alternative to the argument short.panel.labs. Possible values are one of "label_both" (panel labelled by both grouping variable names and levels) and "label_value" (panel labelled with only grouping levels).

Position adjustment, either as a string, or the result of a call to a position adjustment function.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments passed to the function ggpar(), facet() or ggarrange() when printing the plot.

summary stats to display in the table. Possible values are those returned by the function get_summary_stats(), including: "n", "min", "max", "median", "q1", "q2", "q3", "mad", "mean", "sd", "se", "ci".

a ggpubr function, including: ggboxplot, ggviolin, ggdotplot, ggbarplot, ggline, etc. Can be any other ggplot function that accepts the following arguments data, x, color, fill, palette, ggtheme, facet.by.

fill color.

logical. If TRUE, create free plot panels when the argument facet.by is specified.

a numeric vector of length 2, specifying the heights of the main and the summary table, respectively.

the summary table font size.

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none".

a data frame

x and y variables for drawing.

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

text font color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

text font size.

text font style. Allowed values are one of c("plain", "bold", "italic", "bold.italic").

character vector specifying font family.

logical. Should text be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

grouping variables to sort the data by, when the user wants to display the top n up/down labels.

Position adjustment, either as a string, or the result of a call to a position adjustment function.

a ggplot. If not NULL, points are added to an existing plot.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to ggpar.

a data.frame or matrix.

optional vector to specify row names

optional vector to specify column names

optional viewport

a list, as returned by the function ttheme(), defining the parameters of the table theme. Allowed values include one of ttheme() and ttheme_clean().

extra parameters for text justification, e.g.: hjust and x. Default is "centre" for the body and header, and "right" for the row names. Left justification: hjust = 0, x = 0.1. Right justification: hjust = 1, x = 0.9.

character string the table style/theme. The available themes are illustrated in the ggtexttable-theme.pdf file. Allowed values include one of c("default", "blank", "classic", "minimal", "light", "lBlack", "lBlue", "lRed", "lGreen", "lViolet", "lCyan", "lOrange", "lBlackWhite", "lBlueWhite", "lRedWhite", "lGreenWhite", "lVioletWhite", "lCyanWhite", "lOrangeWhite", "mBlack", "mBlue", "mRed", "mGreen", "mViolet", "mCyan", "mOrange", "mBlackWhite", "mBlueWhite", "mRedWhite", "mGreenWhite", "mVioletWhite", "mCyanWhite", "mOrangeWhite" ). Note that, l = "light"; m = "medium".

default font size

default font colour

length-2 unit vector specifying the horizontal and vertical padding of text within each cell

a list, as returned by the function colnames_style(), defining the style of the table column names. Considered only when base_size = "default".

a list, as returned by the function rownames_style(), defining the style of the table row names. Considered only when base_size = "default".

a list, as returned by the function tbody_style(), defining the style of the table body. Considered only when base_size = "default".

text font color, face and size, respectively. Allowed values for face include c("plain", "bold", "italic", "bold.italic").

background color.

line width and color, respectively.

logical, default behaviour for parsing text as plotmath

an object from ggtexttable or from gridExtra::tableGrob().

an integer specifying the row and the column numbers for the cell of interest.

numeric value specifying fill color transparency. Value should be in [0, 1], where 0 is full transparency and 1 is no transparency.

line type

Numeric value in [0, 1] to reduce the size by.

a numeric vector of row indexes; for example at.row = c(1, 2).

row side to which the horinzotal line should be added. Can be one of c("bottom", "top").

integer indicating the column from which to start drawing the horizontal line.

integer indicating the column to which the horizontal line should end.

a numeric vector of column indexes; for example at.column = c(1, 2).

column side to which the vertical line should be added. Can be one of c("left", "right").

integer indicating the row from which to start drawing the horizontal line.

integer indicating the row to which the vertical line should end.

text to be added as title or footnote.

font family

The justification of the text relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". For numeric values, 0 means left (bottom) alignment and 1 means right (top) alignment.

A numeric vector specifying horizontal justification. If specified, overrides the just setting.

A numeric vector specifying vertical justification. If specified, overrides the just setting.

a data frame

character string containing the name of x variable.

character vector containing one or more variables to plot

logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.

logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.

outline color.

fill color.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

color transparency. Values should be between 0 and 1.

plot main title.

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.

a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).

logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.

line types.

If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails.

Numeric value (e.g.: size = 1). change the size of points and outlines.

violin width.

If not(NULL) (default), draw horizontal lines at the given quantiles of the density estimate.

character vector specifying which items to display.

character vector specifying which items to remove from the plot.

character vector specifying the order of items.

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

the name of the column containing point labels. Can be also a character vector with length = nrow(data).

a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").

can be of two formats:

• a character vector specifying some labels to show.

• a list containing one or the combination of the following components:

  • top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).

  • criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

a logical value, whether to use ggrepel to avoid overplotting text labels or not.

logical value. If TRUE, add rectangle underneath the text, making it easier to read.

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

other arguments to be passed to geom_violin, ggpar and facet.

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". Can be also a numeric vector; in this case a basic color palette is created using the function palette.

axis for which grid should be added. Allowed values include c("xy", "x", "y").

grid line color.

numeric value specifying grid line size.

line type. An integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, twodash). Sess show_line_types.

a numeric vector. Each value should be in [0-1]

a numeric vector of length 2 containing the data ranges (minimum and the maximum)

other arguments to pass to coord_flip.

numeric value specifying the rotation angle. Default is 90 for vertical x-axis text.

horizontal justification (in [0, 1]).

vertical justification (in [0, 1]).

other arguments to pass to the function element_text().

character string specifying the plot components. Allowed values include:

• "grid" for both x and y grids

• "x.grid" for x axis grids

• "y.grid" for y axis grids

• "axis" for both x and y axes

• "x.axis" for x axis

• "y.axis" for y axis

• "xlab", or "x.title" for x axis label

• "ylab", or "y.title" for y axis label

• "xylab", "xy.title" or "axis.title" for both x and y axis labels

• "x.text" for x axis texts (x axis tick labels)

• "y.text" for y axis texts (y axis tick labels)

• "xy.text" or "axis.text" for both x and y axis texts

• "ticks" for both x and y ticks

• "x.ticks" for x ticks

• "y.ticks" for y ticks

• "legend.title" for the legend title

• "legend" for the legend

a ggplot

Color palette. Allowed values include:

• Grey color palettes: "grey" or "gray";

• RColorBrewer palettes, see brewer.pal and details section. Examples of palette names include: "RdBu", "Blues", "Dark2", "Set2", ...;

• Custom color palettes. For example, palette = c("#00AFBB", "#E7B800", "#FC4E07");

• ggsci scientific journal palettes, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

other arguments passed to ggplot2 scale_color_xxx() and scale_fill_xxx() functions.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

ANOVA test methods. Possible values are one of c("one_way", "one_way_repeated", "two_way", "two_way_repeated", "two_way_mixed").

(factor) column name containing individuals/subjects identifier. Should be unique per individual. Required only for repeated measure tests ("one_way_repeated", "two_way_repeated", "friedman_test", etc).

(optional) character vector specifying the grouping variable; it should be used only for grouped plots. Possible values are :

• "x.var": Group by the x-axis variable and perform the test between legend groups. In other words, the p-value is compute between legend groups at each x position

• "legend.var": Group by the legend variable and perform the test between x-axis groups. In other words, the test is performed between the x-groups for each legend level.

the type of sums of squares for ANOVA. Allowed values are either 1, 2 or 3. type = 2 is the default because this will yield identical ANOVA results as type = 1 when data are balanced but type = 2 will additionally yield various assumption tests where appropriate. When the data are unbalanced the type = 3 is used by popular commercial softwares including SPSS.

the effect size to compute and to show in the ANOVA results. Allowed values can be either "ges" (generalized eta squared) or "pes" (partial eta squared) or both. Default is "ges".

(optional) for a linear model, an lm model object from which the overall error sum of squares and degrees of freedom are to be calculated. Read more in Anova() documentation.

character. Used only in repeated measures ANOVA test to specify which correction of the degrees of freedom should be reported for the within-subject factors. Possible values are:

• "GG": applies Greenhouse-Geisser correction to all within-subjects factors even if the assumption of sphericity is met (i.e., Mauchly's test is not significant, p > 0.05).

• "HF": applies Hyunh-Feldt correction to all within-subjects factors even if the assumption of sphericity is met,

• "none": returns the ANOVA table without any correction and

• "auto": apply automatically GG correction to only within-subjects factors violating the sphericity assumption (i.e., Mauchly's test p-value is significant, p <= 0.05).

character string specifying label. Can be:

• the column containing the label (e.g.: label = "p" or label = "p.adj"), where p is the p-value. Other possible values are "p.signif", "p.adj.signif", "p.format", "p.adj.format".

• an expression that can be formatted by the glue() package. For example, when specifying label = "Anova, p = \{p\}", the expression {p} will be replaced by its value.

• a combination of plotmath expressions and glue expressions. You may want some of the statistical parameter in italic; for example:label = "Anova, italic(p) = {p}".

• a constant: label = "as_italic": display statistical parameters in italic; label = "as_detailed": detailed plain text; label = "as_detailed_expression" or label = "as_detailed_italic": detailed plotmath expression. Statistical parameters will be displayed in italic.

.

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

• If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".

• If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

numeric value in with the increase in fraction of total height for every additional comparison to minimize overlap. The step value can be negative to reverse the order of groups.

method for adjusting p values (see p.adjust). Has impact only in a situation, where multiple pairwise tests are performed; or when there are multiple grouping variables. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".

a list of arguments specifying the signifcance cutpoints and symbols. For example, significance <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

other arguments to pass to geom_text, such as:

• hjust: horizontal justification of the text. Move the text left or right and

• vjust: vertical justification of the text. Move the text up or down.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

character vector with alternative label, if not null test is ignored

the label type. Can be one of "text" and "expression" (for parsing plotmath expression).

numeric vector with the y positions of the brackets

numeric vector with the positions of the left sides of the brackets

numeric vector with the positions of the right sides of the brackets

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

a variable name for grouping brackets before adding step.increase. Useful to group bracket by facet panel.

numeric vector with the fraction of total height that the bar goes down to indicate the precise column

Vertical adjustment to nudge brackets by. Useful to move up or move down the bracket. If positive value, brackets will be moved up; if negative value, brackets are moved down.

a small numeric value in [0-1] for shortening the with of bracket.

change the width of the lines of the bracket

change the size of the label text

change the font used for the text

move the text up or down relative to the bracket

other arguments passed on to layer. These are often aesthetics, used to set an aesthetic to a fixed value, like color = "red" or size = 3. They may also be parameters to the paired geom/stat.

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

logical. If TRUE, flip x and y coordinates so that horizontal becomes vertical, and vertical, horizontal. When adding the p-values to a horizontal ggplot (generated using coord_flip()), you need to specify the option coord.flip = TRUE.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

the type of central tendency measure to be used. Possible values include: "mean", "median", "mode".

other arguments to pass to geom_line.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

a character string indicating which method to be used for comparing means.

a logical indicating whether you want a paired test. Used only in t.test and in wilcox.test.

a list of additional arguments used for the test method. For example one might use method.args = list(alternative = "greater") for wilcoxon test.

a character string specifying the reference group. If specified, for a given grouping variable, each of the group levels will be compared to the reference group (i.e. control group).

ref.group can be also ".all.". In this case, each of the grouping variable levels is compared to all (i.e. basemean).

A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the groups of interest, to be compared.

logical value. If TRUE, hide ns symbol when displaying significance levels.

a character string to separate the terms. Default is ", ", to separate the correlation coefficient and the p.value.

character string specifying label type. Allowed values include "p.signif" (shows the significance levels), "p.format" (shows the formatted p value).

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

• If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".

• If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

move the text up or down relative to the bracket.

numeric vector with the fraction of total height that the bar goes down to indicate the precise column. Default is 0.03. Can be of same length as the number of comparisons to adjust specifically the tip lenth of each comparison. For example tip.length = c(0.01, 0.03).

If too short they will be recycled.

Width of the lines of the bracket.

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

other arguments to pass to geom_text or geom_label.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

confidence level used to construct the ellipses. By default, 0.95.

number of points used to draw the ellipses.

logical value. If TRUE, the coordinates of the ellipse around the barycentre of individuals are calculated.

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

a character string indicating which correlation coefficient (or covariance) is to be computed. One of "pearson" (default), "kendall", or "spearman".

a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter.

character. Can be one of "R" (pearson coef), "rho" (spearman coef) and "tau" (kendall coef). Uppercase and lowercase are allowed.

a character string to separate the terms. Default is ", ", to separate the correlation coefficient and the p.value.

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

• If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".

• If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

If too short they will be recycled.

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

character One of "expression", "latex", "tex" or "text".

integer indicating the number of decimal places (round) or significant digits (signif) to be used for the correlation coefficient and the p-value, respectively..

a real value specifying the number of decimal places of precision for the correlation coefficient. Default is NULL. Use (e.g.) 0.01 to show 2 decimal places of precision. If specified, then r.digits is ignored.

a real value specifying the number of decimal places of precision for the p-value. Default is NULL. Use (e.g.) 0.0001 to show 4 decimal places of precision. If specified, then p.digits is ignored.

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

other arguments to pass to geom_text or geom_label.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

(factor) column name containing individuals/subjects identifier. Should be unique per individual. Required only for repeated measure tests ("one_way_repeated", "two_way_repeated", "friedman_test", etc).

(optional) character vector specifying the grouping variable; it should be used only for grouped plots. Possible values are :

• "x.var": Group by the x-axis variable and perform the test between legend groups. In other words, the p-value is compute between legend groups at each x position

• "legend.var": Group by the legend variable and perform the test between x-axis groups. In other words, the test is performed between the x-groups for each legend level.

the column containing the label (e.g.: label = "p" or label = "p.adj"), where p is the p-value. Can be also an expression that can be formatted by the glue() package. For example, when specifying label = "t-test, p = {p}", the expression {p} will be replaced by its value.

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

• If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".

• If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

method for adjusting p values (see p.adjust). Has impact only in a situation, where multiple pairwise tests are performed; or when there are multiple grouping variables. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".

a list of arguments specifying the signifcance cutpoints and symbols. For example, significance <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

other arguments passed to the function geom_bracket() or geom_text()

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

(optional) character vector specifying the grouping variable; it should be used only for grouped plots. Possible values are :

• "x.var": Group by the x-axis variable and perform the test between legend groups. In other words, the p-value is compute between legend groups at each x position

• "legend.var": Group by the legend variable and perform the test between x-axis groups. In other words, the test is performed between the x-groups for each legend level.

the column containing the label (e.g.: label = "p" or label = "p.adj"), where p is the p-value. Can be also an expression that can be formatted by the glue() package. For example, when specifying label = "t-test, p = {p}", the expression {p} will be replaced by its value.

can be numeric or character vector of the same length as the number of groups and/or panels. If too short they will be recycled.

• If numeric, value should be between 0 and 1. Coordinates to be used for positioning the label, expressed in "normalized parent coordinates".

• If character, allowed values include: i) one of c('right', 'left', 'center', 'centre', 'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre', 'middle') for y-axis.

numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

method for adjusting p values (see p.adjust). Has impact only in a situation, where multiple pairwise tests are performed; or when there are multiple grouping variables. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".

a list of arguments specifying the signifcance cutpoints and symbols. For example, significance <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

other arguments passed to the function geom_bracket() or geom_text()

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

other arguments to pass to geom_point.

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.