This function the proportion V or J genes used by
grouping variables. This function only quantifies
single gene loci for indicated chain. For
examining VJ pairing, please see percentVJ()
.
percentGenes(
input.data,
chain = "TRB",
gene = "Vgene",
group.by = NULL,
order.by = NULL,
exportTable = FALSE,
palette = "inferno"
)
The product of combineTCR()
,
combineBCR()
, or combineExpression()
.
"TRA", "TRB", "TRG", "TRG", "IGH", "IGL".
"V", "D" or "J"
The variable to use for grouping
A vector of specific plotting order or "alphanumeric" to plot groups in order
Returns the data frame used for forming the graph.
Colors to use in visualization - input any hcl.pals.
ggplot of percentage of indicated genes as a heatmap
#Making combined contig data
combined <- combineTCR(contig_list,
samples = c("P17B", "P17L", "P18B", "P18L",
"P19B","P19L", "P20B", "P20L"))
percentGenes(combined,
chain = "TRB",
gene = "Vgene")