plotClusters: Plot density plots from clutering results.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Plots results from inferHeterogeneity.

Usage

plotClusters(
  clusters,
  tsb = NULL,
  genes = NULL,
  showCNvars = FALSE,
  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.
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)

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.455s elapsed (0.422s cpu) 
Processing TCGA-AB-3009..
Removed 1 variants with no copy number data.
   Hugo_Symbol Chromosome Start_Position End_Position Tumor_Sample_Barcode
1:        PHF6         23      133551224    133551224         TCGA-AB-3009
       t_vaf Segment_Start Segment_End Segment_Mean CN
1: 0.9349112            NA          NA           NA NA
Copy number altered variants:
   Hugo_Symbol Chromosome Start_Position End_Position Tumor_Sample_Barcode
1:     NFKBIL2          8      145668658    145668658         TCGA-AB-3009
2:         NF1         17       29562981     29562981         TCGA-AB-3009
3:       SUZ12         17       30293198     30293198         TCGA-AB-3009
       t_vaf Segment_Start Segment_End Segment_Mean       CN    cluster
1: 0.4415584     145232496   145760746       0.3976 2.634629 CN_altered
2: 0.8419000      29054355    30363868      -0.9157 1.060173 CN_altered
3: 0.8958333      29054355    30363868      -0.9157 1.060173 CN_altered
Warning messages:
1: In if (genes == "CN_altered") { :
  the condition has length > 1 and only the first element will be used
2: In if (genes == "all") { :
  the condition has length > 1 and only the first element will be used

maftools documentation built on Feb. 6, 2021, 2 a.m.