plotMutProfile {MesKit} | R Documentation |
plotMutProfile
plotMutProfile( maf, patient.id = NULL, class = "SP", classByTumor = FALSE, topGenesCount = 10, geneList = NULL, sample.text.size = 11, gene.text.size = 11, legend.text.size = 11, legend.title.size = 11, bgCol = "#f0f0f0", patientsCol = NULL, removeEmptyCols = TRUE, removeEmptyRows = TRUE, showColnames = TRUE, sampleOrder = NULL, use.tumorSampleLabel = FALSE, ... )
maf |
Maf or MafList object generated by |
patient.id |
Select or reorder the patients. Default NULL, all patients are included. Classify SSNVs/Indels into Shared/P-shared/Private, Clonal/Subclonl or Shared-Clonal/P-shared-Clonal/Private-Clonal/Shared-Subclonal/P-shared-SubClonal/Private-SubClonal |
class |
The class which would be represented. Default "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS". |
classByTumor |
Logical (Default: FALSE). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE) |
topGenesCount |
The number of genes print, Default 10. |
geneList |
A list of genes to restrict the analysis. Default NULL. |
sample.text.size |
Fontsize of sample name. Default 11. |
gene.text.size |
Fontsize of gene text. Default 11. |
legend.text.size |
Fontsize of legend text. Default 11. |
legend.title.size |
Fontsize of legend title. Default 11. |
bgCol |
Background grid color. Default "#f0f0f0". |
patientsCol |
A list containing customized colors for distinct patients. Default NULL. |
removeEmptyCols |
Logical (Default: TRUE). Whether remove the samples without alterations. |
removeEmptyRows |
Logical (Default: TRUE). Whether remove the genes without alterations. |
showColnames |
Logical (Default: TRUE). Show sample names of columns. |
sampleOrder |
A named list which contains the sample order used in plotting the final profile. Default NULL. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'. |
... |
Other options passed to |
Mutational profile
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") plotMutProfile(maf, class = "SP")