Visualize proportion across two categorical variables

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",
  ...
)

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".

Value

ggplot or list of ggplot

Examples

plotProportion(pbmcPlot)

plotProportionBar(pbmcPlot, method = "group")

plotProportionPie(pbmcPlot)