Plot gistic results.
takes output generated by readGistic and draws a plot similar to oncoplot.
gisticOncoPlot( gistic = NULL, top = NULL, bands = NULL, showTumorSampleBarcodes = FALSE, gene_mar = 5, barcode_mar = 6, sepwd_genes = 0.5, sepwd_samples = 0.25, clinicalData = NULL, clinicalFeatures = NULL, sortByAnnotation = FALSE, sampleOrder = NULL, annotationColor = NULL, bandsToIgnore = NULL, removeNonAltered = TRUE, colors = NULL, SampleNamefontSize = 0.6, fontSize = 0.8, legendFontSize = 1.2, annotationFontSize = 1.2, borderCol = "white", bgCol = "#CCCCCC" )
gistic |
an |
top |
how many top cytobands to be drawn. defaults to all. |
bands |
draw oncoplot for these bands. Default NULL. |
showTumorSampleBarcodes |
logical to include sample names. |
gene_mar |
Default 5 |
barcode_mar |
Default 6 |
sepwd_genes |
Default 0.5 |
sepwd_samples |
Default 0.25 |
clinicalData |
data.frame with columns containing Tumor_Sample_Barcodes and rest of columns with annotations. |
clinicalFeatures |
columns names from 'clinicalData' to be drawn in the plot. Dafault NULL. |
sortByAnnotation |
logical sort oncomatrix (samples) by provided 'clinicalFeatures'. Defaults to FALSE. column-sort |
sampleOrder |
Manually speify sample names for oncolplot ordering. Default NULL. |
annotationColor |
list of colors to use for clinicalFeatures. Default NULL. |
bandsToIgnore |
do not show these bands in the plot Default NULL. |
removeNonAltered |
Logical. If |
colors |
named vector of colors Amp and Del events. |
SampleNamefontSize |
font size for sample names. Default 0.6 |
fontSize |
font size for cytoband names. Default 0.8 |
legendFontSize |
font size for legend. Default 1.2 |
annotationFontSize |
font size for annotations. Default 1.2 |
borderCol |
Default "white" |
bgCol |
Default "#CCCCCC" |
Takes gistic file as input and plots it as a matrix. Any desired annotations can be added at the bottom of the oncoplot by providing annotation
None.
all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic)
gisticOncoPlot(laml.gistic)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.