mutHeatmap {MesKit} | R Documentation |
plot binary or CCF heatmap of somatic mutations.
mutHeatmap( maf, patient.id = NULL, min.vaf = 0, min.ccf = 0, use.adjVAF = FALSE, use.ccf = FALSE, geneList = NULL, plot.geneList = FALSE, show.geneList = TRUE, mut.threshold = 50, sample.text.size = 9, legend.title.size = 10, gene.text.size = 9, sampleOrder = NULL, use.tumorSampleLabel = FALSE, classByTumor = FALSE, ... )
maf |
Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
min.vaf |
The minimum value of VAF. Default 0. Option: on the scale of 0 to 1. |
min.ccf |
The minimum value of CCF. Default 0. Option: on the scale of 0 to 1. |
use.adjVAF |
Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE. |
use.ccf |
Logical. If FALSE (Default: FALSE), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap. |
geneList |
List of genes to restrict the analysis. Default NULL. |
plot.geneList |
Logical (Default: FALSE). If TRUE, plot heatmap with genes on geneList when geneList is not NULL. |
show.geneList |
Show the names of gene on the geneList. Default TRUE. |
mut.threshold |
show.gene and show.geneList will be FALSE when patient have more mutations than threshold. Default 150. |
sample.text.size |
Size of sample name.Default 9. |
legend.title.size |
Size of legend title.Default 10. |
gene.text.size |
Size of gene text. Default 9. |
sampleOrder |
A named list which contains the sample order used in plotting the heatmap. Default NULL. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
classByTumor |
Logical Default: FALSE. Classify mutations based on "Tumor_ID". |
... |
Other options passed to |
heatmap of somatic mutations
maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit") clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit") ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit") maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19") mutHeatmap(maf)