coOncoplot: Draw two oncoplots side by side for cohort comparision.

In maftools: Summarize, Analyze and Visualize MAF Files

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,
  sortByAnnotation1 = FALSE,
  sortByAnnotation2 = FALSE,
  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 = "#CCCCCC",
  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
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
sampleOrder1	Manually speify sample names in m1 for oncolplot ordering. Default NULL.
sampleOrder2	Manually speify 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

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()

Example output

-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 45 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.245s elapsed (0.218s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.109s elapsed (0.106s cpu) 
null device 
          1 

maftools documentation built on Feb. 6, 2021, 2 a.m.