gisticOncoPlot {maftools} | 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,
      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)

[Package maftools version 2.6.05 Index]