Compare V or J gene distributions

This function compares the V or J gene usages between given groups.

Usage

plotGeneUsage(
  x,
  level = c("V", "J"),
  scale = c("count", "frequency"),
  colorBy = NULL,
  facetBy = NULL,
  label_colors = NULL,
  show_stats = FALSE
)

Arguments

x

an object of class RepSeqExperiment

level

a character specifying the level of the repertoire to be taken into account when calculating the gene usages. Should be one of "aaClone" or "ntClone".

scale

a character specifying whether to plot the gene usage in "count" or "frequency".

colorBy

a character indicating a column name in mData. Colors are thus attributed to the different groups within this column. The chosen column must be of class factor.

facetBy

a vector of character indicating one or two column names in mData to apply a facet on.

label_colors

a list of colors for each variable in ColorBy. See plotColors. If NULL, default colors are used.

show_stats

whether to statistically compare groups

Examples

data(RepSeqData)

plotGeneUsage(x = RepSeqData, 
              level = "J", 
              scale = "count", 
              colorBy = "cell_subset", 
              show_stats=TRUE )
#> [1] "Performing Wilcoxon test with Bonferroni correction for 2 groups"


plotGeneUsage(x = RepSeqData,
             level = "V", 
             scale = "frequency",
             colorBy = "cell_subset", 
             facetBy="sex")