coOncoplot: Draw two oncoplots side by side for cohort comparision.
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

coOncoplot

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,
  annotationFontSize = 1.2,
  sortByM1 = FALSE,
  sortByM2 = FALSE,
  sortByAnnotation1 = FALSE,
  annotationOrder1 = NULL,
  sortByAnnotation2 = FALSE,
  annotationOrder2 = NULL,
  sampleOrder1 = NULL,
  sampleOrder2 = NULL,
  additionalFeature1 = NULL,
  additionalFeaturePch1 = 20,
  additionalFeatureCol1 = "white",
  additionalFeatureCex1 = 0.9,
  additionalFeature2 = NULL,
  additionalFeaturePch2 = 20,
  additionalFeatureCol2 = "white",
  additionalFeatureCex2 = 0.9,
  sepwd_genes1 = 0.5,
  sepwd_samples1 = 0.5,
  sepwd_genes2 = 0.5,
  sepwd_samples2 = 0.5,
  colors = NULL,
  removeNonMutated = TRUE,
  anno_height = 2,
  legend_height = 4,
  geneNamefont = 0.8,
  showSampleNames = FALSE,
  SampleNamefont = 0.5,
  barcode_mar = 1,
  outer_mar = 3,
  gene_mar = 1,
  legendFontSize = 1.2,
  titleFontSize = 1.5,
  keepGeneOrder = FALSE,
  bgCol = "#ecf0f1",
  borderCol = "white"
)

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.
`annotationFontSize`	font size for annotations Default 1.2
`sortByM1`	sort by mutation frequency in 'm1'
`sortByM2`	sort by mutation frequency in 'm2'
`sortByAnnotation1`	logical sort oncomatrix (samples) by provided 'clinicalFeatures1'. Sorts based on first 'clinicalFeatures1'. Defaults to FALSE. column-sort
`annotationOrder1`	Manually specify order for annotations for 'clinicalFeatures1'. Works only for first value. Default NULL.
`sortByAnnotation2`	same as above but for m2
`annotationOrder2`	Manually specify order for annotations for 'clinicalFeatures2'. Works only for first value. Default NULL.
`sampleOrder1`	Manually specify sample names in m1 for oncolplot ordering. Default NULL.
`sampleOrder2`	Manually specify sample names in m2 for oncolplot ordering. Default NULL.
`additionalFeature1`	a vector of length two indicating column name in the MAF and the factor level to be highlighted.
`additionalFeaturePch1`	Default 20
`additionalFeatureCol1`	Default "white"
`additionalFeatureCex1`	Default 0.9
`additionalFeature2`	a vector of length two indicating column name in the MAF and the factor level to be highlighted.
`additionalFeaturePch2`	Default 20
`additionalFeatureCol2`	Default "white"
`additionalFeatureCex2`	Default 0.9
`sepwd_genes1`	Default 0.5
`sepwd_samples1`	Default 0.5
`sepwd_genes2`	Default 0.5
`sepwd_samples2`	Default 0.5
`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`.
`anno_height`	Height of clinical margin. Default 2
`legend_height`	Height of legend margin. Default 4
`geneNamefont`	font size for gene names. Default 1
`showSampleNames`	whether to show sample names. Defult FALSE.
`SampleNamefont`	font size for sample names. Default 0.5
`barcode_mar`	Margin width for sample names. Default 1
`outer_mar`	Margin width for outer. Default 3
`gene_mar`	Margin width for gene names. Default 1
`legendFontSize`	font size for legend. Default 1.2
`titleFontSize`	font size for title. Default 1.5
`keepGeneOrder`	force the resulting plot to use the order of the genes as specified. 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 'white'

Details

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

Value

Invisibly returns a list of sample names in their order of occurrences in M1 and M2 respectively.

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()

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