dot-ggplotLigerTheme: Generic ggplot theme setting for rliger package

In rliger: Linked Inference of Genomic Experimental Relationships

Generic ggplot theme setting for rliger package

Description

Controls content and size of all peripheral texts.

Usage

.ggplotLigerTheme(
  plot,
  title = NULL,
  subtitle = NULL,
  xlab = TRUE,
  ylab = TRUE,
  xlabAngle = 0,
  legendColorTitle = NULL,
  legendFillTitle = NULL,
  legendShapeTitle = NULL,
  legendSizeTitle = NULL,
  showLegend = TRUE,
  legendPosition = "right",
  baseSize = getOption("ligerBaseSize"),
  titleSize = NULL,
  subtitleSize = NULL,
  xTextSize = NULL,
  xFacetSize = NULL,
  xTitleSize = NULL,
  yTextSize = NULL,
  yFacetSize = NULL,
  yTitleSize = NULL,
  legendTextSize = NULL,
  legendTitleSize = NULL,
  legendDotSize = 4,
  panelBorder = FALSE,
  legendNRow = NULL,
  legendNCol = NULL,
  colorLabels = NULL,
  colorValues = NULL,
  colorPalette = "magma",
  colorDirection = -1,
  naColor = "#DEDEDE",
  colorLow = NULL,
  colorMid = NULL,
  colorHigh = NULL,
  colorMidPoint = NULL,
  plotly = FALSE
)

Arguments

plot	ggplot object passed from wrapper plotting functions
title, subtitle, xlab, ylab	Main title, subtitle or X/Y axis title text. By default, no main title or subtitle will be set, and X/Y axis title will be the names of variables used for plotting. Use NULL to hide elements. TRUE for xlab or ylab shows default values.
xlabAngle	Numeric, counter-clockwise rotation angle of X axis label text. Default 0 shows horizontal text.
legendColorTitle	Legend title text for color aesthetics, often used for categorical or continuous coloring of dots. Default NULL shows the original variable name.
legendFillTitle	Legend title text for fill aesthetics, often used for violin, box, bar plots. Default NULL shows the original variable name.
legendShapeTitle	Legend title text for shape aesthetics, often used for shaping dots by categorical variable. Default NULL shows the original variable name.
legendSizeTitle	Legend title text for size aesthetics, often used for sizing dots by continuous variable. Default NULL shows the original variable name.
showLegend	Whether to show the legend. Default TRUE.
legendPosition	Text indicating where to place the legend. Choose from "top", "bottom", "left" or "right". Default "right".
baseSize	One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this.
titleSize, xTitleSize, yTitleSize, legendTitleSize	Size of main title, axis titles and legend title. Default NULL controls by baseSize + 2.
subtitleSize, xTextSize, yTextSize, legendTextSize	Size of subtitle text, axis texts and legend text. Default NULL controls by baseSize.
xFacetSize	Size of facet strip label text on x-axis. Default NULL controls by baseSize - 2.
yFacetSize	Size of facet strip label text on y-axis. Default NULL controls by baseSize - 2.
legendDotSize	Allow dots in legend region to be large enough to see the colors/shapes clearly. Default 4.
panelBorder	Whether to show rectangle border of the panel instead of using ggplot classic bottom and left axis lines. Default FALSE.
legendNRow, legendNCol	Integer, when too many categories in one variable, arranges number of rows or columns. Default NULL, automatically split to ceiling(levels(variable)/15) columns.
colorLabels	Character vector for modifying category names in a color legend. Passed to ggplot2::scale_color_manual(labels). Default NULL uses original levels of the factor.
colorValues	Character vector of colors for modifying category colors in a color legend. Passed to ggplot2::scale_color_manual(values). Default NULL uses internal selected palette when <= 26 categories are presented, otherwise ggplot hues.
colorPalette	For continuous coloring, an index or a palette name to select from available options from ggplot scale_brewer or viridis. Default "magma".
colorDirection	Choose 1 or -1. Applied when colorPalette is from Viridis options. Default -1 use darker color for higher value, while 1 reverses this direction.
naColor	The color code for NA values. Default "#DEDEDE". scale_colour_gradient2. Default NULL.
colorLow, colorMid, colorHigh, colorMidPoint	All four of these must be specified to customize palette with
plotly	Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Value

Updated ggplot object by default. When plotly = TRUE, returns plotly (htmlwidget) object.

rliger documentation built on Oct. 30, 2024, 1:07 a.m.