vizGenes: Visualizing the distribution of gene usage

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Visualizing the distribution of gene usage

Description

This function will allow for the visualizing the distribution of the any VDJ and C gene of the TCR or BCR using heatmap or bar chart. This function requires assumes two chains were used in defining clone, if not, it will default to the only chain present regardless of the chain parameter.

Usage

vizGenes(
  input.data,
  x.axis = "TRBV",
  y.axis = NULL,
  group.by = NULL,
  plot = "heatmap",
  order = "gene",
  scale = TRUE,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR(), combineBCR(), or combineExpression().
x.axis	Gene segments to separate the x-axis, such as "TRAV", "TRBD", "IGKJ".
y.axis	Variable to separate the y-axis, can be both categorical or other gene gene segments, such as "TRAV", "TRBD", "IGKJ".
group.by	Variable in which to group the diversity calculation.
plot	The type of plot to return - heatmap or barplot.
order	Categorical variable to organize the x-axis, either "gene" or "variance"
scale	Converts the individual count of genes to proportion using the total respective repertoire size
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot bar diagram or heatmap of gene usage

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

vizGenes(combined, 
         x.axis = "TRBV",
         y.axis = NULL,
         plot = "heatmap")

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.