box plot of cell population frequencies
plot_frequency_boxplot.Rdplot_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,
statistics = F,
sig_label = "p.adj.signif"
)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.
- statistics
optional string indicating if and which statistics are displayed in the plot. Currently, "wilcox", "t_test" or "diffcyt" are accepted as input. If no statistics should be displayed, set to FALSE.
- sig_label
string indicating how the significance is indicated: "p.adj" for the numerical adjusted p-value, "p.adj.signif" for asteriks.