A value or the magrittr placeholder.

A function call using the magrittr semantics.

tibble

assign colors according to this column

a vector of color values

if colors are not enough, fill na values

presets name

number of colors

other arguments of RColorBrewer::brewer.pal

cm value

cm value

ggplot object

params

params

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 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")

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.

Other arguments passed on to ggplot2::geom_segment().

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().

position of the label brackets

the increase height for next bracket, a ratio according to the whole panel height

the length for tips at the ends of the brackets, a ratio according to the whole panel height

Line end style (round, butt, square).

which values will be add on the plot, a character vector with some of ⁠psymbol, p, right_deno_fc, left_deno_fc⁠ in it. If comparisons is assigned, you can also include ⁠fc1, fc2⁠

if show psymbol in the label, justify the NS labels to make the lineheights look balanced

if TRUE will ignore all label items if p >= 0.05, or you can assign a character vector like cp_label to ignore some items of the label

fold change method, default is mean. If you use log10 or log2 axis, default is geom_mean.

a list of two-element vector, to assign the comparisons should be performed

paired test or not, FALSE as default. If TRUE, you should use mapping=aes(paired_by=col) to indicate pairs by an extra column

one of ⁠two.sided, greater, less⁠

wilcoxon as default, one of ⁠wilcoxon, t⁠

the symbol of non-significant, NS as default

reference item, the others will be compared with it

draw in line or not, default is FALSE

widen the brackets, can be a negative value

fold change digits

comparation result tibble

manual comparisons table, please refer to extract_compare()

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 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")

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().

Line end style (round, butt, square).

show error symbol

one of ⁠point, bar⁠

if center_symbol='bar', the width of the bar

the width of the error bar

the center function, mean as default

the low error function, mean minus sd as default

the high error function, mean plus sd as default

Other arguments passed on to ggplot2::point() or ggplot2::geom_segment.

colors

number of colors to output

inch value

inch value

line point in geom or theme

mm value

mm value

width

height

resolution, 300 as default

alias of width

alias of height

default theme

ggplot object

filename

plot width

plot height

units, 'in' for inch as default. Can be 'in', 'cm'

NULL as default, pass character to use built-in canvas ('A4', 'A4v'), or pass a numeric vector in 'c(width, heigh)' form

from 0 to 1, the horizontal position of plot in canvas

from 0 to 1, the vertical position of plot in canvas

other arguments from ggsave

width

height

resolution, 300 as default

alias of width

alias of height

color values

color number of each row

use vector names as label, FALSE to show the color value

float range, a ratio according to the whole panel height

float cycle

float range, a ratio according to the whole panel height

float cycle

pt value

pt value

ScaleContinuousPosition object, e.g. scales$y in compute_group()

output level

value of base level

vector of element scales

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

One of:

• NULL for no breaks

• waiver() for the default breaks computed by the transformation object

• A numeric vector of positions

• A function that takes the limits as input and returns breaks as output (e.g., a function returned by scales::extended_breaks()). Also accepts rlang lambda function notation.

One of:

• NULL for no minor breaks

• waiver() for the default breaks (one minor break between each major break)

• A numeric vector of positions

• A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation.

An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if breaks = waiver(). Use NULL to use the default number of breaks given by the transformation.

One of:

• NULL for no labels

• waiver() for the default labels computed by the transformation object

• A character vector giving labels (must be same length as breaks)

• An expression vector (must be the same length as breaks). See ?plotmath for details.

• A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

One of:

• NULL to use the default scale range

• A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum

• A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).

use expansion() to dismiss the blank between x axis low limit and y axis

use scales::oob_keep instead of scales::oob_censor, which will always consider the data points out of the limits

Missing values will be replaced with this value.

For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".

A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called ⁠<name>_trans⁠ (e.g., scales::boxcox_trans()). You can create your own transformation with scales::trans_new().

A function used to create a guide or its name. See guides() for more information.

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

sec_axis() is used to specify a secondary axis.

show minor breaks or not

the step of minor breaks

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

One of:

• NULL for no breaks

• waiver() for the default breaks computed by the transformation object

• A numeric vector of positions

• A function that takes the limits as input and returns breaks as output (e.g., a function returned by scales::extended_breaks()). Also accepts rlang lambda function notation.

One of:

• NULL for no minor breaks

• waiver() for the default breaks (one minor break between each major break)

• A numeric vector of positions

• A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation.

An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if breaks = waiver(). Use NULL to use the default number of breaks given by the transformation.

One of:

• NULL for no labels

• waiver() for the default labels computed by the transformation object

• A character vector giving labels (must be same length as breaks)

• An expression vector (must be the same length as breaks). See ?plotmath for details.

• A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

One of:

• NULL to use the default scale range

• A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum

• A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).

use expansion() to dismiss the blank between x axis low limit and y axis

use scales::oob_keep instead of scales::oob_censor, which will always consider the data points out of the limits

Missing values will be replaced with this value.

For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".

A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called ⁠<name>_trans⁠ (e.g., scales::boxcox_trans()). You can create your own transformation with scales::trans_new().

A function used to create a guide or its name. See guides() for more information.

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

sec_axis() is used to specify a secondary axis.

show minor breaks or not

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

One of:

• NULL for no breaks

• waiver() for the default breaks computed by the transformation object

• A numeric vector of positions

• A function that takes the limits as input and returns breaks as output (e.g., a function returned by scales::extended_breaks()). Also accepts rlang lambda function notation.

One of:

• NULL for no minor breaks

• waiver() for the default breaks (one minor break between each major break)

• A numeric vector of positions

• A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation.

An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if breaks = waiver(). Use NULL to use the default number of breaks given by the transformation.

One of:

• NULL for no labels

• waiver() for the default labels computed by the transformation object

• A character vector giving labels (must be same length as breaks)

• An expression vector (must be the same length as breaks). See ?plotmath for details.

• A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

One of:

• NULL to use the default scale range

• A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum

• A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).

use expansion() to dismiss the blank between y axis low limit and x axis

use scales::oob_keep instead of scales::oob_censor, which will always consider the data points out of the limits

Missing values will be replaced with this value.

For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".

A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called ⁠<name>_trans⁠ (e.g., scales::boxcox_trans()). You can create your own transformation with scales::trans_new().

A function used to create a guide or its name. See guides() for more information.

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

sec_axis() is used to specify a secondary axis.

show minor breaks or not

the step of minor breaks

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

One of:

• NULL for no breaks

• waiver() for the default breaks computed by the transformation object

• A numeric vector of positions

• A function that takes the limits as input and returns breaks as output (e.g., a function returned by scales::extended_breaks()). Also accepts rlang lambda function notation.

One of:

• NULL for no minor breaks

• waiver() for the default breaks (one minor break between each major break)

• A numeric vector of positions

• A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation.

An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if breaks = waiver(). Use NULL to use the default number of breaks given by the transformation.

One of:

• NULL for no labels

• waiver() for the default labels computed by the transformation object

• A character vector giving labels (must be same length as breaks)

• An expression vector (must be the same length as breaks). See ?plotmath for details.

• A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

One of:

• NULL to use the default scale range

• A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum

• A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).

use expansion() to dismiss the blank between y axis low limit and x axis

use scales::oob_keep instead of scales::oob_censor, which will always consider the data points out of the limits

Missing values will be replaced with this value.

For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".

A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called ⁠<name>_trans⁠ (e.g., scales::boxcox_trans()). You can create your own transformation with scales::trans_new().

A function used to create a guide or its name. See guides() for more information.

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

sec_axis() is used to specify a secondary axis.

show minor breaks or not

presets name

number of colors

alpha

base size of fonts and margins

base linewidth

base linewidth of the rectangles

a vector of element size scales, namely:

1. base size, used by legend text, axis text, caption

2. used by legend title, axis title, strip text (facet title), subtitle

3. used by title, tag

factor to adjust the element margins according to size_scales

factor to adjust the plot margins according to size_scales[3]

factor to adjust the space of legend items according to size_scales[2]

font family

arguments from ggplot2::theme()

arguments of theme_pl()

text point in geom

ScaleContinuousPosition object, e.g. scales$y in compute_group()