lengthContig: Demonstrate the distribution of lengths filtered contigs.

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

Description

This function takes the output of combineTCR(), combineBCR(), or expression2List() and displays either the nucleotide (nt) or amino acid (aa) sequence length. The sequence length visualized can be selected using the chains parameter, either the combined clonotype (both chains) or across all single chains. Visualization can either be a histogram 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

lengthContig(
  df,
  cloneCall = "aa",
  group = NULL,
  scale = FALSE,
  chains = "combined",
  exportTable = FALSE
)

Arguments

df	The product of combineTCR(), combineBCR(), or expression2List()
cloneCall	How to call the clonotype - CDR3 nucleotide (nt), CDR3 amino acid (aa).
group	The group header for which you would like to analyze the data.
scale	Converts the graphs into denisty plots in order to show relative distributions.
chains	Whether to keep clonotypes "combined" or visualize by chain.
exportTable	Returns the data frame used for forming the graph.

Value

ggplot of the discrete or relative length distributions of clonotype sequences

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")
lengthContig(combined, cloneCall="aa", chains = "combined")

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