vizVgenes: Visualizing the distribution of TCR V gene usage

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

Description

This function will allow for the visualizing the distribution ofthe V-genes of the TCR by categroical variables.

Usage

vizVgenes(
  df,
  TCR = "TCR1",
  facet.x = "sample",
  facet.y = NULL,
  fill = NULL,
  exportTable = FALSE
)

Arguments

df	The product of combineTCR(), combineBCR(), or expression2List().
TCR	Which TCR chain to use, TCR1 = TCRA or TCR2 = TCRB
facet.x	Categorical variable which to seperate by along x-axis
facet.y	Categorical variable which to seperate by along y-axis
fill	Categorical variable which to add color to bar chart
exportTable	Returns the data frame used for forming the graph.

Value

ggplot bar diagram of vgene counts

Examples

#Making combined contig data
x <- contig_list
combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

vizVgenes(combined, TCR = "TCR1", facet.x = "sample")

scRepertoire documentation built on Nov. 8, 2020, 7 p.m.