clonesizeDistribution {scRepertoire} | R Documentation |
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.
clonesizeDistribution( df, cloneCall = "gene+nt", method = "ward.D2", exportTable = FALSE )
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. |
ggplot dendrogram of the clone size distribution
#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")