Plot distribution of discrete variables

Visualizes the count or the proportion of barcode spots falling into certain groups via barcharts. It does so either for the whole sample or in a comparing manner if across is specified.

plotBarchart(
  object,
  grouping_variables,
  across = NULL,
  across_subset = NULL,
  relevel = NULL,
  clrp = NULL,
  clrp_adjust = NULL,
  position = "stack",
  display_facets = NULL,
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

across

Character value or NULL. Specifies the grouping variable of interest.

Use getGroupingOptions() to obtain all variable names that group the barcode spots of your object in a certain manner.

across_subset

Character vector or NULL. Specifies the particular groups of interest the grouping variable specified in argument across contains.

If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.)

Use getGroupNames() to obtain all valid input options.

relevel

Logical value. If set to TRUE the input order of across_subset determines the order in which the groups of interest are displayed. Groups that are not included are dropped which affects the colors with which they are displayed.

clrp

Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.

clrp_adjust

Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.

display_facets

Logical value. If set to TRUE the plot is split via ggplot2::facet_wrap() such that each variable gets it's own subplot.

nrow, ncol

Numeric values or NULL. Used to arrange multiple plots.

...

Additional arguments given to the respective ggplot2::geom_<plot_type>() function. E.g. plotViolinplot() relies on ggplot2::geom_violin().

variables

Character vector. The discrete features whose group count or proportion you want to display. Must not contain the feature specified in across - if across is not set to NULL.

Value

Returns a ggplot that can be additionally customized according to the rules of the ggplot2 framework.

Examples

library(SPATA2)
library(tidyverse)

data("example_data")

object <- example_data$object_UKF275T_diet

plotBarchart(object, grouping_variables = c("seurat_clusters", "bayes_space"))