plotClones: Plot clonal assignment of single cells

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Plot clonal assignment of single cells

Description

Creates a heatmap of single cell mutation calls, clustered using PhISCS.

Usage

plotClones(mutcalls, what = c("alleleFreq", "ternary"), show = c(), ...)

Arguments

mutcalls	object of class mutationCalls.
what	One of the following: alleleFreq: The fraction of reads mapping to the mutant allele or ternary: Ternarized mutation status
show	boolean vector specifying for each mutation if it should be plotted on top of the heatmap as metadata; defaults to mutations not used for the clustering !mutcalls@cluster
...	any arguments passed to pheatmap

Value

Returns TRUE only used for generating a PostScript tree image of the putative mutation tree

Examples

P1 <-
readRDS(system.file("extdata/sample_example1.RDS",package =
"mitoClone2"))
plotClones(P1)

benstory/mitoClone2 documentation built on Nov. 8, 2023, 12:13 a.m.