gisticOncoPlot: Plot gistic results.

Description Usage Arguments Details Value See Also Examples

View source: R/gisticOncoPlot.R

Description

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

Usage

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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

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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.