abundanceContig: Demonstrate the relative abundance of clonotypes by group or...

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

Description

This function takes the output of combineTCR(), combineBCR(), or expression2List() and displays the number of clonotypes at specific frequencies by sample or group. Visualization can either be a line graph using calculated numbers or if scale = TRUE, the output will be a density plot. Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.

Usage

abundanceContig(
  df,
  cloneCall = "gene+nt",
  scale = FALSE,
  group = NULL,
  exportTable = FALSE
)

Arguments

df	The product of combineTCR(), combineBCR(), or expression2List().
cloneCall	How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or C DR3 gene+nucleotide (gene+nt).
scale	Converts the graphs into denisty plots in order to show relative distributions.
group	The column header for which you would like to analyze the data.
exportTable	Exports a table of the data into the global environment in addition to the visualization.

Value

ggplot of the total or relative adundance of clonotypes across quanta

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")
abundanceContig(combined, cloneCall = "gene", scale = FALSE)

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