gisticOncoPlot: Plot gistic results.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

takes output generated by readGistic and draws a plot similar to oncoplot.

Usage

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"
)

Arguments

gistic	an GISTIC object generated by readGistic
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 TRUE removes samples with no mutations in the oncoplot for better visualization. Default FALSE.
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"

Details

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

Value

None.

See Also

oncostrip

Examples

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)

Example output

-Processing Gistic files..
--Processing amp_genes.conf_99.txt
--Processing del_genes.conf_99.txt
--Processing scores.gistic
--Summarizing by samples

maftools documentation built on Feb. 6, 2021, 2 a.m.