plotGeneBar: barplot of each VDJ gene usages

Description Usage Arguments Value

View source: R/visualization.R

Description

barplot of each VDJ gene usages

Usage

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plotGeneBar(btcr, group, sample = "sample", gene = c("v", "j", "c"),
  dtype = c("percentage", "count"), isoform = TRUE, combine = TRUE,
  rotate = TRUE, ncol = 1)

Arguments

btcr

A BTCR object.

group

Column in btcr$contigs to group each VDJ genes, always be sample or group.

sample

The sample column in btcr$contigs.

gene

Plot v_gene, j_gene or c_gene.

dtype

Plot barcode usage counts or percentages.

isoform

If set TRUE, plot the gene isoforms like TRAV-xxx. Or just plot the main gene like TRA, TRB (isoforms are summed.).

combine

Wrap plots togother. Or return the plot list.

rotate

Rotate the x labels.

ncol

When plot isoform, plot ncol in the layout.

Value

A ggplot or ggplot list or patchwork wrapped plot.


xizhihui/BTCR documentation built on Dec. 23, 2021, 7:10 p.m.