oncostrip {maftools} | R Documentation |
draw an oncostrip similar to cBioportal oncoprinter output.
oncostrip(maf, genes = NULL, top = 5, colors = NULL, sort = TRUE, clinicalFeatures = NULL, annotationDat = NULL, sortByAnnotation = FALSE, annotationOrder = NULL, removeNonMutated = TRUE, showTumorSampleBarcodes = FALSE, annotationColor = NULL, fontSize = 10, titleFontSize = 15, legendFontSize = 12, bgCol = "#CCCCCC", borderCol = NA)
maf |
an |
genes |
draw oncoprint for these genes. default NULL. Plots top 5 genes. |
top |
how many top genes to be drawn. defaults to 5. |
colors |
named vector of colors for each Variant_Classification. |
sort |
logical sort oncomatrix for enhanced visualization. Defaults to TRUE. |
clinicalFeatures |
columns names from 'clinical.data' slot of |
annotationDat |
If MAF file was read without annotations, provide a custom |
sortByAnnotation |
logical sort oncomatrix (samples) by provided 'clinicalFeatures' Defaults to FALSE. column-sort. |
annotationOrder |
Manually specify order for annotations. Works only for first 'clinicalFeatures'. Default NULL. |
removeNonMutated |
Logical. If |
showTumorSampleBarcodes |
logical to include sample names. |
annotationColor |
list of colors to use for 'clinicalFeatures'. Must be a named list. Default NULL. |
fontSize |
font size for gene names. Default 10. |
titleFontSize |
font size for title. Default 15 |
legendFontSize |
font size for legend. Default 12 |
bgCol |
Background grid color for wild-type (not-mutated) samples. Default gray - "#CCCCCC" |
borderCol |
border grid color for wild-type (not-mutated) samples. Default NA. |
None.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) dev.new() oncostrip(maf = laml, genes = c('NPM1', 'RUNX1'))