plotCNA {MesKit} | R Documentation |
plotCNA
plotCNA( seg, patient.id = NULL, sampleOrder = NULL, chrSilent = NULL, refBuild = "hg19", sample.text.size = 11, chrom.text.size = 3, legend.text.size = 9, legend.title.size = 11, annot.text.size = 3, sample.bar.height = 0.5, chrom.bar.height = 0.5, showRownames = TRUE, removeEmptyChr = TRUE, showCytoband = FALSE, showGene = FALSE, use.tumorSampleLabel = FALSE )
seg |
Object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
sampleOrder |
A named list which contains the sample order used in plotting the final profile. Default NULL. |
chrSilent |
Chromosomes excluded in the analysis. e.g, 1, 2, 3. Default NULL. |
refBuild |
Human reference genome versions of hg18, hg19 or hg38 by UCSC. Default "hg19". |
sample.text.size |
Fontsize of sample name. Default 11. |
chrom.text.size |
Fontsize of chromosome text. Default 3. |
legend.text.size |
Fontsize of legend text. Default 9. |
legend.title.size |
Fontsize of legend title. Default 11. |
annot.text.size |
Fontsize of cytoband or gene symbols. Default 3. |
sample.bar.height |
Bar height of each sample. Default 0.5. |
chrom.bar.height |
Bar height of each chromosome. Default 0.5. |
showRownames |
Logical (Default: TRUE). Show sample names of rows. |
removeEmptyChr |
Remove empty chromosomes that do not exist in all samples. Default TRUE. |
showCytoband |
Logical (Default: FALSE). Show cytobands on the plot. Only when the seg object is created with GISTIC results, this parameter can be TRUE. |
showGene |
Logical (Default: FALSE). Show gene symbols on the plot. Only when the seg object is created with txdb, this parameter can be TRUE. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'. |
a heatmap plot of CNA profile
segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit") seg <- readSegment(segFile = segFile) plotCNA(seg) ## showCytoband gisticAmpGenesFile <- system.file("extdata", "COREAD_amp_genes.conf_99.txt", package = "MesKit") gisticDelGenesFile <- system.file("extdata", "COREAD_del_genes.conf_99.txt", package = "MesKit") gisticAllLesionsFile <- system.file("extdata", "COREAD_all_lesions.conf_99.txt", package = "MesKit") seg <- readSegment(segFile = segFile, gisticAmpGenesFile = gisticAmpGenesFile, gisticDelGenesFile = gisticDelGenesFile, gisticAllLesionsFile = gisticAllLesionsFile) plotCNA(seg, showCytoband = TRUE)