clonesizeDistribution: Hierarchical clustering of clonotypes on clonotype size and...

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

Description

This functionn produces a heirachial clustering of clonotypes by sample using the Jensen-Shannon distance and discrete gamma-GPD spliced threshold model in the [powerTCR R package] (https://bioconductor.org/packages/devel/bioc/html/powerTCR.html). Please read and cite PMID: 30485278 if using the function for analyses. If a matrix output for the data is preferred set exportTable = TRUE.

Usage

clonesizeDistribution(
  df,
  cloneCall = "gene+nt",
  method = "ward.D2",
  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 CDR3 gene+nucleotide (gene+nt).
method	The clustering paramater for the dendrogram.
exportTable	Returns the data frame used for forming the graph.

Value

ggplot dendrogram of the clone size distribution

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")
clonesizeDistribution(combined, cloneCall = "gene+nt", method="ward.D2")

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