coOncoplot {maftools} | R Documentation

## Draw two oncoplots side by side for cohort comparision.

### Description

Draw two oncoplots side by side for cohort comparision.

### Usage

    coOncoplot(m1, m2, genes = NULL, m1Name = NULL, m2Name = NULL,
      clinicalFeatures1 = NULL, clinicalFeatures2 = NULL,
      annotationColor1 = NULL, annotationColor2 = NULL,
      sortByAnnotation1 = FALSE, sortByAnnotation2 = FALSE, colors = NULL,
      removeNonMutated = TRUE, geneNamefont = 10, showSampleNames = FALSE,
      SampleNamefont = 10, legendFontSize = 10, titleFontSize = 12,
      keepGeneOrder = FALSE, includeSyn = FALSE, bgCol = "#CCCCCC",
      borderCol = NA)

### Arguments

`m1` | first `MAF` object
`m2` | second `MAF` object
`genes` | draw these genes. Default plots top 5 mutated genes from two cohorts.
`m1Name` | optional name for first cohort
`m2Name` | optional name for second cohort
`clinicalFeatures1` | columns names from 'clinical.data' slot of m1 `MAF` to be drawn in the plot. Dafault NULL.
`clinicalFeatures2` | columns names from 'clinical.data' slot of m2 `MAF` to be drawn in the plot. Dafault NULL.
`annotationColor1` | list of colors to use for 'clinicalFeatures1' Default NULL.
`annotationColor2` | list of colors to use for 'clinicalFeatures2' Default NULL.
`sortByAnnotation1` | logical sort oncomatrix (samples) by provided 'clinicalFeatures1'. Sorts based on first 'clinicalFeatures1'. Defaults to FALSE. column-sort
`sortByAnnotation2` | same as above but for m2
`colors` | named vector of colors for each Variant_Classification.
`removeNonMutated` | Logical. If `TRUE` removes samples with no mutations in the oncoplot for better visualization. Default `TRUE`.
`geneNamefont` | font size for gene names. Default 10
`showSampleNames` | whether to show sample names. Defult FALSE.
`SampleNamefont` | font size for sample names. Default 10
`legendFontSize` | font size for legend. Default 10
`titleFontSize` | font size for title. Default 12
`keepGeneOrder` | force the resulting plot to use the order of the genes as specified. Default FALSE
`includeSyn` | Set to TRUE to include silent variants. Default FALSE.
`bgCol` | Background grid color for wild-type (not-mutated) samples. Default gray - "#CCCCCC"
`borderCol` | border grid color for wild-type (not-mutated) samples. Default NA.

### Details

Draws two oncoplots side by side to display difference between two cohorts.

### Value

Returns nothing. Just draws plot.

### Examples

    #' ##Primary and Relapse APL
    primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
    relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
    ##Read mafs
    primary.apl <- read.maf(maf = primary.apl)
    relapse.apl <- read.maf(maf = relapse.apl)
    ##Plot
    coOncoplot(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary APL', m2Name = 'Relapse APL')
    dev.off()

[Package maftools version 1.6.15 Index]