gisticOncoPlot: Plot gistic results.
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

gisticOncoPlot

R Documentation

Plot gistic results.

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,
  right_mar = 2.5,
  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
`right_mar`	Default 2.5
`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.

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)

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.