Package 'plutor' reference manual

Title:	Useful Functions for Visualization
Description:	In ancient Roman mythology, 'Pluto' was the ruler of the underworld and presides over the afterlife. 'Pluto' was frequently conflated with 'Plutus', the god of wealth, because mineral wealth was found underground. When plotting with R, you try once, twice, practice again and again, and finally you get a pretty figure you want. It's a 'plot tour', a tour about repetition and reward. Hope 'plutor' helps you on the tour!
Authors:	William Song [aut, cre]
Maintainer:	William Song <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.0
Built:	2025-02-20 04:30:51 UTC
Source:	https://github.com/william-swl/plutor

assign colors by a column in a tibble, for the convenience to use `scale_color_identity()`

Description

assign colors by a column in a tibble, for the convenience to use scale_color_identity()

Usage

assign_colors(df, by, colors = sci_colors("npg", 10), na = "#F5F5F5")
assign_colors(df, by, colors = sci_colors("npg", 10), na = "#F5F5F5")

Arguments

`df`	tibble
`by`	assign colors according to this column
`colors`	a vector of color values
`na`	if colors are not enough, fill na values

Value

tibble

Examples

assign_colors(mini_diamond, cut, colors = sci_colors("nejm", 8))
assign_colors(mini_diamond, cut, colors = sci_colors("nejm", 8))

colors of nucleotides and amino acids

Description

colors of nucleotides and amino acids

Usage

bioletter_colors
bioletter_colors

Format

`bioletter_colors`

colors for biological letters like amino acids or nucleotides

Source

according to the print format

select colors from `RColorBrewer` package presets

Description

select colors from RColorBrewer package presets

Usage

brewer_colors(name, n = 3, ...)
brewer_colors(name, n = 3, ...)

Arguments

`name`	presets name
`n`	number of colors
`...`	other arguments of `RColorBrewer::brewer.pal`

Value

colors

Examples

brewer_colors("Blues", 5)
brewer_colors("Blues", 5)

width and height of built-in canvas

Description

width and height of built-in canvas

Usage

canvas_size
canvas_size

Format

`canvas_size`

canvas sizes list

Source

according to the print format

trans cm to inch

Description

trans cm to inch

Usage

cm2inch(x)
cm2inch(x)

Arguments

x

cm value

Value

inch value

Examples

cm2inch(1)
cm2inch(1)

trans cm to pt

Description

trans cm to pt

Usage

cm2pt(x)
cm2pt(x)

Arguments

x

cm value

Value

pt value

Examples

cm2pt(1)
cm2pt(1)

extract the result of `geom_compare` from a `ggplot` object

Description

extract the result of geom_compare from a ggplot object

Usage

extract_compare(p)
extract_compare(p)

Arguments

`p`	ggplot object

Value

compare tibble

add p value and fold change on a plot

Description

add p value and fold change on a plot

Usage

geom_compare(
  mapping = NULL,
  data = NULL,
  stat = "compare",
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lab_pos = NULL,
  step_increase = 0.1,
  tip_length = 0.02,
  lineend = "round",
  cp_label = c("psymbol"),
  ns_lineheight_just = 0.2,
  ignore_ns = FALSE,
  fc_method = NULL,
  comparisons = NULL,
  paired = FALSE,
  alternative = "two.sided",
  test_method = "wilcoxon",
  ns_symbol = "NS",
  cp_ref = NULL,
  cp_inline = FALSE,
  brackets_widen = 0,
  fc_digits = 2,
  cp_result = NULL,
  cp_manual = NULL
)
geom_compare(
  mapping = NULL,
  data = NULL,
  stat = "compare",
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lab_pos = NULL,
  step_increase = 0.1,
  tip_length = 0.02,
  lineend = "round",
  cp_label = c("psymbol"),
  ns_lineheight_just = 0.2,
  ignore_ns = FALSE,
  fc_method = NULL,
  comparisons = NULL,
  paired = FALSE,
  alternative = "two.sided",
  test_method = "wilcoxon",
  ns_symbol = "NS",
  cp_ref = NULL,
  cp_inline = FALSE,
  brackets_widen = 0,
  fc_digits = 2,
  cp_result = NULL,
  cp_manual = NULL
)

Arguments

`mapping`	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.
`data`	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)`).
`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"`)
`position`	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()`.
`na.rm`	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
`show.legend`	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.
`inherit.aes`	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()`.
`lab_pos`	position of the label brackets
`step_increase`	the increase height for next bracket, a ratio according to the whole panel height
`tip_length`	the length for tips at the ends of the brackets, a ratio according to the whole panel height
`lineend`	Line end style (round, butt, square).
`cp_label`	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`
`ns_lineheight_just`	if show `psymbol` in the label, justify the `NS` labels to make the lineheights look balanced
`ignore_ns`	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
`fc_method`	fold change method, default is `mean`. If you use `log10` or `log2` axis, default is `geom_mean`.
`comparisons`	a list of two-element vector, to assign the comparisons should be performed
`paired`	paired test or not, `FALSE` as default. If `TRUE`, you should use mapping=aes(paired_by=col) to indicate pairs by an extra column
`alternative`	one of `⁠two.sided, greater, less⁠`
`test_method`	`wilcoxon` as default, one of `⁠wilcoxon, t⁠`
`ns_symbol`	the symbol of non-significant, `NS` as default
`cp_ref`	reference item, the others will be compared with it
`cp_inline`	draw in line or not, default is `FALSE`
`brackets_widen`	widen the brackets, can be a negative value
`fc_digits`	fold change digits
`cp_result`	comparation result tibble
`cp_manual`	manual comparisons table, please refer to `extract_compare()`

Value

ggplot object

The describe geom is used to create description values plot, including center symbol and error symbol. The center symbol can be mean, median or other custom functions, the error symbol can be sd, quantile or other custom functions.

Usage

geom_describe(
  mapping = NULL,
  data = NULL,
  stat = "describe",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lineend = "round",
  show_error = TRUE,
  center_symbol = "bar",
  center_width = 0.3,
  error_width = 0.2,
  center_func = mean,
  low_func = function(x, na.rm) {
     mean(x, na.rm = na.rm) - sd(x, na.rm = na.rm)
 },
  high_func = function(x, na.rm) {
     mean(x, na.rm = na.rm) + sd(x, na.rm = na.rm)
 },
  ...
)
geom_describe(
  mapping = NULL,
  data = NULL,
  stat = "describe",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lineend = "round",
  show_error = TRUE,
  center_symbol = "bar",
  center_width = 0.3,
  error_width = 0.2,
  center_func = mean,
  low_func = function(x, na.rm) {
     mean(x, na.rm = na.rm) - sd(x, na.rm = na.rm)
 },
  high_func = function(x, na.rm) {
     mean(x, na.rm = na.rm) + sd(x, na.rm = na.rm)
 },
  ...
)

Arguments

`mapping`	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.
`data`	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)`).
`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"`)
`position`	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.
`na.rm`	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
`show.legend`	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.
`inherit.aes`	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()`.
`lineend`	Line end style (round, butt, square).
`show_error`	show error symbol
`center_symbol`	one of `⁠point, bar⁠`
`center_width`	if `center_symbol='bar'`, the width of the bar
`error_width`	the width of the error bar
`center_func`	the center function, `mean` as default
`low_func`	the low error function, `mean` minus `sd` as default
`high_func`	the high error function, `mean` plus `sd` as default
`...`	Other arguments passed on to `ggplot2::point()` or `ggplot2::geom_segment`.

Value

ggplot object

geom2trace.GeomCompare

Description

geom2trace.GeomCompare

Usage

geom2trace.GeomCompare(data, params, plot)
geom2trace.GeomCompare(data, params, plot)

Arguments

data, params, plot

params

Value

no return value

geom2trace.GeomDescribe

Description

geom2trace.GeomDescribe

Usage

geom2trace.GeomDescribe(data, params, plot)
geom2trace.GeomDescribe(data, params, plot)

Arguments

data, params, plot

params

Value

no return value

GeomCompare

Description

GeomCompare

Usage

GeomCompare
GeomCompare

Format

An object of class GeomCompare (inherits from Geom, ggproto, gg) of length 6.

GeomDescribe

Description

GeomDescribe

Usage

GeomDescribe
GeomDescribe

Format

An object of class GeomDescribe (inherits from Geom, ggproto, gg) of length 5.

generate gradient colors

Description

generate gradient colors

Usage

gradient_colors(x, n)
gradient_colors(x, n)

Arguments

`x`	colors
`n`	number of colors to output

Value

gradient colors

Examples

gradient_colors(c("blue", "red"), 10)
gradient_colors(c("blue", "red"), 10)

trans inch to cm

Description

trans inch to cm

Usage

inch2cm(x)

in2cm(x)

cm2in(x)
inch2cm(x)

in2cm(x)

cm2in(x)

Arguments

`x`	inch value

Value

cm value

Examples

inch2cm(1)
inch2cm(1)

trans inch to mm

Description

trans inch to mm

Usage

inch2mm(x)

in2mm(x)
inch2mm(x)

in2mm(x)

Arguments

`x`	inch value

Value

mm value

Examples

inch2mm(1)
inch2mm(1)

trans geom line point and theme line point to the real point

Description

trans geom line point and theme line point to the real point

Usage

lpt(x)
lpt(x)

Arguments

`x`	line point in geom or theme

Value

real point

Examples

lpt(1)
lpt(1)

Minimal tibble dataset adjusted from diamond

Description

Minimal tibble dataset adjusted from diamond

Usage

mini_diamond
mini_diamond

Format

`mini_diamond`

A data frame with 100 rows and 7 columns:

id: unique id
cut, clarity: 2 category variables
carat, price, x, y: 4 continuous variables

...

Source

adjusted from ggplot2

trans mm to inch

Description

trans mm to inch

Usage

mm2inch(x)

mm2in(x)
mm2inch(x)

mm2in(x)

Arguments

x

mm value

Value

inch value

Examples

mm2inch(1)
mm2inch(1)

trans mm to pt

Description

trans mm to pt

Usage

mm2pt(x)
mm2pt(x)

Arguments

x

mm value

Value

pt value

Examples

mm2pt(1)
mm2pt(1)

set size, resolution and default theme

Description

set size, resolution and default theme

Usage

pl_init(
  width = 4,
  height = 3,
  res = 300,
  w = NULL,
  h = NULL,
  theme = theme_pl()
)
pl_init(
  width = 4,
  height = 3,
  res = 300,
  w = NULL,
  h = NULL,
  theme = theme_pl()
)

Arguments

`width`	width
`height`	height
`res`	resolution, 300 as default
`w`	alias of width
`h`	alias of height
`theme`	default theme

Value

no return value

Examples

pl_init()
pl_init()

save plot, support save into a blank canvas

Description

save plot, support save into a blank canvas

Usage

pl_save(
  plot,
  filename,
  width,
  height,
  units = "in",
  canvas = NULL,
  canvas_pos_x = 0.5,
  canvas_pos_y = 0.1,
  ...
)
pl_save(
  plot,
  filename,
  width,
  height,
  units = "in",
  canvas = NULL,
  canvas_pos_x = 0.5,
  canvas_pos_y = 0.1,
  ...
)

Arguments

`plot`	ggplot object
`filename`	filename
`width`	plot width
`height`	plot height
`units`	units, 'in' for inch as default. Can be 'in', 'cm'
`canvas`	`NULL` as default, pass character to use built-in canvas ('A4', 'A4v'), or pass a numeric vector in 'c(width, heigh)' form
`canvas_pos_x`	from 0 to 1, the horizontal position of plot in canvas
`canvas_pos_y`	from 0 to 1, the vertical position of plot in canvas
`...`	other arguments from `ggsave`

Value

no return value

set repr size and resolution

Description

set repr size and resolution

Usage

pl_size(width = 4, height = 3, res = 300, w = NULL, h = NULL)
pl_size(width = 4, height = 3, res = 300, w = NULL, h = NULL)

Arguments

`width`	width
`height`	height
`res`	resolution, 300 as default
`w`	alias of width
`h`	alias of height

Value

no return value

Examples

pl_size(width = 3, height = 2)
pl_size(width = 3, height = 2)

plot colors

Description

plot colors

Usage

plot_colors(x, ncol = 10, show_name = TRUE)
plot_colors(x, ncol = 10, show_name = TRUE)

Arguments

`x`	color values
`ncol`	color number of each row
`show_name`	use vector names as label, `FALSE` to show the color value

Value

ggplot object

Examples

plot_colors(gradient_colors(c("blue", "red"), 10))
plot_colors(gradient_colors(c("blue", "red"), 10))

a new Position object to create float x position

Description

a new Position object to create float x position

Usage

position_floatxPL(float = -0.05, cycle = 2)
position_floatxPL(float = -0.05, cycle = 2)

Arguments

`float`	float range, a ratio according to the whole panel height
`cycle`	float cycle

Value

Position object

a new Position object to create float y position

Description

a new Position object to create float y position

Usage

position_floatyPL(float = -0.05, cycle = 2)
position_floatyPL(float = -0.05, cycle = 2)

Arguments

`float`	float range, a ratio according to the whole panel height
`cycle`	float cycle

Value

Position object

PositionFloatxPL

Description

PositionFloatxPL

Usage

PositionFloatxPL
PositionFloatxPL

Format

An object of class PositionFloatxPL (inherits from Position, ggproto, gg) of length 4.

PositionFloatyPL

Description

PositionFloatyPL

Usage

PositionFloatyPL
PositionFloatyPL

Format

An object of class PositionFloatyPL (inherits from Position, ggproto, gg) of length 4.

trans pt to cm

Description

trans pt to cm

Usage

pt2cm(x)
pt2cm(x)

Arguments

x

pt value

Value

cm value

Examples

pt2cm(1)
pt2cm(1)

trans pt to mm

Description

trans pt to mm

Usage

pt2mm(x)
pt2mm(x)

Arguments

x

pt value

Value

mm value

Examples

pt2mm(1)
pt2mm(1)

revert the position scale transformation

Description

revert the position scale transformation

Usage

revert_pos_scale(s)
revert_pos_scale(s)

Arguments

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

Value

function

scale element according to a vector of element scales

Description

scale element according to a vector of element scales

Usage

scale_ele(level, base, ele_scales)
scale_ele(level, base, ele_scales)

Arguments

`level`	output level
`base`	value of base level
`ele_scales`	vector of element scales

Value

value of output level

Examples

scale_ele(level = 2, base = 5, ele_scales = c(1, 2))
scale_ele(level = 2, base = 5, ele_scales = c(1, 2))

A variant of `scale_x_continuous()` to show axis minor breaks

Description

A variant of scale_x_continuous() to show axis minor breaks

Usage

scale_x_continuous_pl(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = waiver(),
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = "identity",
  guide = ggh4x::guide_axis_minor(),
  position = "bottom",
  sec.axis = waiver(),
  show_minor_breaks = TRUE,
  minor_break_step = NULL
)
scale_x_continuous_pl(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = waiver(),
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = "identity",
  guide = ggh4x::guide_axis_minor(),
  position = "bottom",
  sec.axis = waiver(),
  show_minor_breaks = TRUE,
  minor_break_step = NULL
)

Arguments

`name`	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.
`breaks`	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.
`minor_breaks`	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.
`n.breaks`	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.
`labels`	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.
`limits`	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()`).
`expand`	use `expansion()` to dismiss the blank between x axis low limit and y axis
`oob`	use `scales::oob_keep` instead of `scales::oob_censor`, which will always consider the data points out of the limits
`na.value`	Missing values will be replaced with this value.
`trans`	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()`.
`guide`	A function used to create a guide or its name. See `guides()` for more information.
`position`	For position scales, The position of the axis. `left` or `right` for y axes, `top` or `bottom` for x axes.
`sec.axis`	`sec_axis()` is used to specify a secondary axis.
`show_minor_breaks`	show minor breaks or not
`minor_break_step`	the step of minor breaks

Value

scale object

A variant of `scale_x_log10()` to show axis minor breaks and better axis labels

Description

A variant of scale_x_log10() to show axis minor breaks and better axis labels

Usage

scale_x_log10_pl(
  name = waiver(),
  breaks = NULL,
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = NULL,
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = scales::log10_trans(),
  guide = ggh4x::guide_axis_minor(),
  position = "bottom",
  sec.axis = waiver(),
  show_minor_breaks = TRUE
)
scale_x_log10_pl(
  name = waiver(),
  breaks = NULL,
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = NULL,
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = scales::log10_trans(),
  guide = ggh4x::guide_axis_minor(),
  position = "bottom",
  sec.axis = waiver(),
  show_minor_breaks = TRUE
)

Arguments

`name`	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.
`breaks`	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.
`minor_breaks`	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.
`n.breaks`	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.
`labels`	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.
`limits`	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()`).
`expand`	use `expansion()` to dismiss the blank between x axis low limit and y axis
`oob`	use `scales::oob_keep` instead of `scales::oob_censor`, which will always consider the data points out of the limits
`na.value`	Missing values will be replaced with this value.
`trans`	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()`.
`guide`	A function used to create a guide or its name. See `guides()` for more information.
`position`	For position scales, The position of the axis. `left` or `right` for y axes, `top` or `bottom` for x axes.
`sec.axis`	`sec_axis()` is used to specify a secondary axis.
`show_minor_breaks`	show minor breaks or not

Value

scale object

A variant of `scale_y_continuous()` to show axis minor breaks

Description

A variant of scale_y_continuous() to show axis minor breaks

Usage

scale_y_continuous_pl(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = waiver(),
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = "identity",
  guide = ggh4x::guide_axis_minor(),
  position = "left",
  sec.axis = waiver(),
  show_minor_breaks = TRUE,
  minor_break_step = NULL
)
scale_y_continuous_pl(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = waiver(),
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = "identity",
  guide = ggh4x::guide_axis_minor(),
  position = "left",
  sec.axis = waiver(),
  show_minor_breaks = TRUE,
  minor_break_step = NULL
)

Arguments

`name`	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.
`breaks`	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.
`minor_breaks`	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.
`n.breaks`	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.
`labels`	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.
`limits`	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()`).
`expand`	use `expansion()` to dismiss the blank between y axis low limit and x axis
`oob`	use `scales::oob_keep` instead of `scales::oob_censor`, which will always consider the data points out of the limits
`na.value`	Missing values will be replaced with this value.
`trans`	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()`.
`guide`	A function used to create a guide or its name. See `guides()` for more information.
`position`	For position scales, The position of the axis. `left` or `right` for y axes, `top` or `bottom` for x axes.
`sec.axis`	`sec_axis()` is used to specify a secondary axis.
`show_minor_breaks`	show minor breaks or not
`minor_break_step`	the step of minor breaks

Value

scale object

A variant of `scale_y_log10()` to show axis minor breaks and better axis labels

Description

A variant of scale_y_log10() to show axis minor breaks and better axis labels

Usage

scale_y_log10_pl(
  name = waiver(),
  breaks = NULL,
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = NULL,
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = scales::log10_trans(),
  guide = ggh4x::guide_axis_minor(),
  position = "left",
  sec.axis = waiver(),
  show_minor_breaks = TRUE
)
scale_y_log10_pl(
  name = waiver(),
  breaks = NULL,
  minor_breaks = NULL,
  n.breaks = NULL,
  labels = NULL,
  limits = NULL,
  expand = ggplot2::expansion(),
  oob = scales::oob_keep,
  na.value = NA_real_,
  trans = scales::log10_trans(),
  guide = ggh4x::guide_axis_minor(),
  position = "left",
  sec.axis = waiver(),
  show_minor_breaks = TRUE
)

Arguments

`name`	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.
`breaks`	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.
`minor_breaks`	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.
`n.breaks`	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.
`labels`	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.
`limits`	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()`).
`expand`	use `expansion()` to dismiss the blank between y axis low limit and x axis
`oob`	use `scales::oob_keep` instead of `scales::oob_censor`, which will always consider the data points out of the limits
`na.value`	Missing values will be replaced with this value.
`trans`	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()`.
`guide`	A function used to create a guide or its name. See `guides()` for more information.
`position`	For position scales, The position of the axis. `left` or `right` for y axes, `top` or `bottom` for x axes.
`sec.axis`	`sec_axis()` is used to specify a secondary axis.
`show_minor_breaks`	show minor breaks or not

Value

scale object

select colors from `ggsci` package presets

Description

select colors from ggsci package presets

Usage

sci_colors(name, n = 3, alpha = 1)
sci_colors(name, n = 3, alpha = 1)

Arguments

`name`	presets name
`n`	number of colors
`alpha`	alpha

Value

colors

Examples

sci_colors("npg", 5)
sci_colors("npg", 5)

StatCompare

Description

StatCompare

Usage

StatCompare
StatCompare

Format

An object of class StatCompare (inherits from Stat, ggproto, gg) of length 6.

StatCountPL

Description

StatCountPL

Usage

StatCountPL
StatCountPL

Format

An object of class StatCountPL (inherits from Stat, ggproto, gg) of length 4.

StatDescribe

Description

StatDescribe

Usage

StatDescribe
StatDescribe

Format

An object of class StatDescribe (inherits from Stat, ggproto, gg) of length 4.

StatFuncPL

Description

StatFuncPL

Usage

StatFuncPL
StatFuncPL

Format

An object of class StatFuncPL (inherits from Stat, ggproto, gg) of length 4.

StatMeanPL

Description

StatMeanPL

Usage

StatMeanPL
StatMeanPL

Format

An object of class StatMeanPL (inherits from Stat, ggproto, gg) of length 4.

a new extensible theme

Description

a new extensible theme

Usage

theme_pl(
  base_size = 10,
  base_line_size = lpt(base_size/10),
  base_rect_size = lpt(1),
  size_scales = c(5, 6, 7),
  margin_factor = 0.25,
  plot_margin_factor = 0.5,
  legend_spacing_factor = 1.2,
  font_family = "",
  ...
)
theme_pl(
  base_size = 10,
  base_line_size = lpt(base_size/10),
  base_rect_size = lpt(1),
  size_scales = c(5, 6, 7),
  margin_factor = 0.25,
  plot_margin_factor = 0.5,
  legend_spacing_factor = 1.2,
  font_family = "",
  ...
)

Arguments

`base_size`	base size of fonts and margins
`base_line_size`	base linewidth
`base_rect_size`	base linewidth of the rectangles
`size_scales`	a vector of element size scales, namely: base size, used by legend text, axis text, caption used by legend title, axis title, strip text (facet title), subtitle used by title, tag
`margin_factor`	factor to adjust the element margins according to size_scales
`plot_margin_factor`	factor to adjust the plot margins according to `size_scales[3]`
`legend_spacing_factor`	factor to adjust the space of legend items according to `size_scales[2]`
`font_family`	font family
`...`	arguments from ggplot2::theme()

Value

theme object of ggplot

Examples

theme_pl()
theme_pl()

a blank theme

Description

a blank theme

Usage

theme_pl0(...)
theme_pl0(...)

Arguments

...

arguments of theme_pl()

Value

theme object of ggplot

Examples

theme_pl0()
theme_pl0()

trans geom text or point to the real point

Description

trans geom text or point to the real point

Usage

tpt(x)

ppt(x)
tpt(x)

ppt(x)

Arguments

`x`	text point in geom

Value

real point

Examples

tpt(1)
tpt(1)

perform the position scale transformation

Description

perform the position scale transformation

Usage

trans_pos_scale(s)
trans_pos_scale(s)

Arguments

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

Value

function

Package 'plutor'

Help Index

assign colors by a column in a tibble, for the convenience to use scale_color_identity()

Description

Usage

Arguments

Value

Examples

colors of nucleotides and amino acids

Description

Usage

Format

bioletter_colors

Source

select colors from RColorBrewer package presets

Description

Usage

Arguments

Value

Examples

width and height of built-in canvas

Description

Usage

Format

canvas_size

Source

trans cm to inch

Description

Usage

Arguments

Value

Examples

trans cm to pt

Description

Usage

Arguments

Value

Examples

extract the result of geom_compare from a ggplot object

Description

Usage

Arguments

Value

add p value and fold change on a plot

Description

Usage

Arguments

Value

Description values plot

Description

Usage

Arguments

Value

geom2trace.GeomCompare

Description

Usage

Arguments

Value

geom2trace.GeomDescribe

Description

Usage

Arguments

Value

GeomCompare

Description

Usage

Format

GeomDescribe

Description

Usage

Format

generate gradient colors

Description

Usage

Arguments

Value

Examples

trans inch to cm

Description

Usage

assign colors by a column in a tibble, for the convenience to use `scale_color_identity()`

`bioletter_colors`

select colors from `RColorBrewer` package presets

`canvas_size`

extract the result of `geom_compare` from a `ggplot` object

`mini_diamond`