% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggplotting.R
\name{.ggplotLigerTheme}
\alias{.ggplotLigerTheme}
\title{Generic ggplot theme setting for rliger package}
\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{
\item{plot}{ggplot object passed from wrapper plotting functions}

\item{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 \code{NULL} to hide elements.
\code{TRUE} for \code{xlab} or \code{ylab} shows default values.}

\item{xlabAngle}{Numeric, counter-clockwise rotation angle of X axis label
text. Default \code{0} shows horizontal text.}

\item{legendColorTitle}{Legend title text for color aesthetics, often used
for categorical or continuous coloring of dots. Default \code{NULL} shows the
original variable name.}

\item{legendFillTitle}{Legend title text for fill aesthetics, often used for
violin, box, bar plots. Default \code{NULL} shows the original variable name.}

\item{legendShapeTitle}{Legend title text for shape aesthetics, often used
for shaping dots by categorical variable. Default \code{NULL} shows the
original variable name.}

\item{legendSizeTitle}{Legend title text for size aesthetics, often used for
sizing dots by continuous variable. Default \code{NULL} shows the original
variable name.}

\item{showLegend}{Whether to show the legend. Default \code{TRUE}.}

\item{legendPosition}{Text indicating where to place the legend. Choose from
\code{"top"}, \code{"bottom"}, \code{"left"} or \code{"right"}. Default
\code{"right"}.}

\item{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.}

\item{titleSize, xTitleSize, yTitleSize, legendTitleSize}{Size of main title,
axis titles and legend title. Default \code{NULL} controls by
\code{baseSize + 2}.}

\item{subtitleSize, xTextSize, yTextSize, legendTextSize}{Size of subtitle text,
axis texts and legend text. Default \code{NULL} controls by \code{baseSize}.}

\item{xFacetSize, yFacetSize}{Size of facet label text. Default \code{NULL}
controls by \code{baseSize - 2}.}

\item{legendDotSize}{Allow dots in legend region to be large enough to see
the colors/shapes clearly. Default \code{4}.}

\item{panelBorder}{Whether to show rectangle border of the panel instead of
using ggplot classic bottom and left axis lines. Default \code{FALSE}.}

\item{legendNRow, legendNCol}{Integer, when too many categories in one
variable, arranges number of rows or columns. Default \code{NULL},
automatically split to \code{ceiling(levels(variable)/10)} columns.}

\item{colorLabels}{Character vector for modifying category names in a
color legend. Passed to \code{ggplot2::scale_color_manual(labels)}. Default
\code{NULL} uses original levels of the factor.}

\item{colorValues}{Character vector of colors for modifying category colors
in a color legend. Passed to \code{ggplot2::scale_color_manual(values)}.
Default \code{NULL} uses internal selected palette when <= 26 categories are
presented, otherwise ggplot hues.}

\item{colorPalette}{For continuous coloring, an index or a palette name to
select from available options from ggplot
\code{\link[ggplot2]{scale_brewer}} or \code{\link[viridisLite]{viridis}}.
Default \code{"magma"}.}

\item{colorDirection}{Choose \code{1} or \code{-1}. Applied when
\code{colorPalette} is from Viridis options. Default \code{-1} use darker
color for higher value, while \code{1} reverses this direction.}

\item{naColor}{The color code for \code{NA} values. Default \code{"#DEDEDE"}.
\code{\link[ggplot2]{scale_colour_gradient2}}. Default \code{NULL}.}

\item{colorLow, colorMid, colorHigh, colorMidPoint}{All four of these must be
specified to customize palette with}

\item{plotly}{Whether to use plotly to enable web based interactive browsing
for the plot. Requires installation of package "plotly". Default
\code{FALSE}.}
}
\value{
Updated ggplot object by default. When \code{plotly = TRUE}, returns
plotly (htmlwidget) object.
}
\description{
Controls content and size of all peripheral texts.
}
