Generic ggplot theme setting for rliger package

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, 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: 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.