.ggplotLigerTheme {rliger}

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,
  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.

legendColorTitle, legendFillTitle, legendShapeTitle, legendSizeTitle

Set alternative title text for legend on aes of color, fill, shape and size, respectively. 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, yFacetSize

Size of facet label text. 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)/10) columns.

colorLabels, colorValues

Each a vector with as many values as the number of categories for the categorical coloring aesthetics. Labels will be the shown text and values will be the color code. These are passed to scale_color_manual. Default uses an internal selected palette if there are <= 26 colors needed, or ggplot hues otherwise, and plot original labels (levels of the factor).

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.