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plot_frequency_boxplot() plots cell population frequencies of samples grouped by group_var as boxplots.

Usage

plot_frequency_boxplot(
  fcd,
  cluster_slot,
  cluster_var,
  sample_var,
  group_var,
  groups_to_show = NULL,
  numeric = F,
  color_palette = cluster_palette,
  dot_size = 2
)

Arguments

fcd

flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR

cluster_slot

string specifying which clustering slot to use to find variable specified in cluster_var

cluster_var

string specifying variable name in cluster_slot that identifies cell population labels to be used (e.g. clusters, metaclusters or predicted labels).

sample_var

string indicating variable name in cell_anno that defines sample IDs to be used.

group_var

string indicating variable name in cell_anno that should be used to group samples in sample_var

groups_to_show

vector of strings indicating levels in group_var that should be included for plotting. By default all groups are plotted.

numeric

logical, if TRUE numeric levels in cluster_var are ordered in increasing order and "Cluster_" is pasted before number, if FALSE alphabetical ordering is applied.

color_palette

vector of colors to be used to fill box plots

dot_size

Size of the dots.

Value

plot_frequency_boxplots() returns a list of boxplots, each element of the list contains the plot of one cell population.

Details

plot_frequency_boxplot