rliger (version 2.0.1)

plotProportion: Visualize proportion across two categorical variables

Description

plotProportionBar creates bar plots comparing the cross-category proportion. plotProportionDot creates dot plots. plotClusterProportions has variable pre-specified and calls the dot plot. plotProportion produces a combination of both bar plots and dot plot.

Having package "ggrepel" installed can help adding tidier percentage annotation on the pie chart.

Usage

plotProportion(
  object,
  class1 = NULL,
  class2 = "dataset",
  method = c("stack", "group", "pie"),
  ...
)
plotProportionDot(
  object,
  class1 = NULL,
  class2 = "dataset",
  showLegend = FALSE,
  panelBorder = TRUE,
  ...
)
plotProportionBar(
  object,
  class1 = NULL,
  class2 = "dataset",
  method = c("stack", "group"),
  inclRev = FALSE,
  panelBorder = TRUE,
  combinePlot = TRUE,
  ...
)
plotClusterProportions(object, useCluster = NULL, return.plot = FALSE, ...)
plotProportionPie(
  object,
  class1 = NULL,
  class2 = "dataset",
  labelSize = 4,
  labelColor = "white",
  ...
)

Value

ggplot or list of ggplot

Arguments

object

A liger object.

class1, class2

Each should be a single name of a categorical variable available in cellMeta slot. Number of cells in each categories in class2 will be served as the denominator when calculating proportions. By default class1 = NULL and uses default clusters and class2 = "dataset".

method

For bar plot, choose whether to draw "stack" or "group" bar plot. Default "stack".

showLegend, panelBorder, ...

ggplot theme setting arguments passed to .ggplotLigerTheme.

inclRev

Logical, for barplot, whether to reverse the specification for class1 and class2 and produce two plots. Default FALSE.

combinePlot

Logical, whether to combine the two plots with plot_grid when two plots are created. Default TRUE.

useCluster

For plotClusterProportions. Same as class1 while class2 is hardcoded with "dataset".

return.plot

defuncted.

labelSize, labelColor

Settings on pie chart percentage label. Default 4 and "white".

Examples

plotProportion(pbmcPlot)
plotProportionBar(pbmcPlot, method = "group")
plotProportionPie(pbmcPlot)