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,
  variables,
  phase = NULL,
  across = NULL,
  across_subset = NULL,
  relevel = TRUE,
  clrp = "milo",
  clrp_adjust = NULL,
  position = "fill",
  display_facets = TRUE,
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

object	A valid cypro object.
variables	Character vector. The grouping variables whose group count or proportion you want to display. Must not contain the feature specified in across - if across is not set to NULL.
phase	Character or numeric. If character, the ordinal value referring to the phase of interest (e.g. 'first', 'second' etc.). referring to the phase of interest or 'all'. If numeric, the number referring to the phase. If set to NULL takes the phase denoted as default with adjustDefault(). Ignored if the experiment design contains only one phase.
across	Character value, character vector or NULL (see details for more). Specifies the grouping variable of interest. Use getGroupingVariableNames() to obtain all variable names that group the cells of your experiment 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 choice of color.
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.
ncol	Given to ggplot2::facet_wrap(). Affects the way the subplots are displayed.
nrow	Given to ggplot2::facet_wrap(). Affects the way the subplots are displayed.
...	Additional arguments given to the respective ggplot2::geom_<plot_type>() function. E.g. plotViolinplot() relies on ggplot2::geom_violin().

Value

A ggplot.