plotClusters {maftools} | R Documentation

## Plot density plots from clutering results.

### Description

Plots results from inferHeterogeneity.

### Usage

    plotClusters(clusters, tsb = NULL, genes = NULL, showCNvars = FALSE,
      savePlot = FALSE, width = 6, height = 5, colors = NULL)

### Arguments

`clusters` | clustering results from `inferHeterogeneity`
`tsb` | sample to plot from clustering results. Default plots all samples from results.
`genes` | genes to highlight on the plot. Can be a vector of gene names, `CN_altered` to label copy number altered varinats. or `all` to label all genes. Default NULL.
`showCNvars` | show copy numbered altered variants on the plot. Default FALSE.
`savePlot` | If TRUE saves plot to output pdf
`width` | plot width. Default 6.
`height` | plot height. Default 5.
`colors` | manual colors for clusters. Default NULL.

### Value

returns nothing.

### See Also

`inferHeterogeneity`

### Examples

    ## Not run:
    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    seg = system.file('extdata', 'TCGA.AB.3009.hg19.seg.txt', package = 'maftools')
    TCGA.AB.3009.clust <- inferHeterogeneity(maf = laml, tsb = 'TCGA-AB-3009',
    segFile = seg, vafCol = 'i_TumorVAF_WU')
    plotClusters(TCGA.AB.3009.clust, genes = c('NF1', 'SUZ12'), showCNvars = TRUE)

    ## End(Not run)

[Package maftools version 1.8.0 Index]