coBarplot: Draw two barplots side by side for cohort comparision.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Draw two barplots side by side for cohort comparision.

Usage

coBarplot(
  m1,
  m2,
  genes = NULL,
  orderBy = NULL,
  m1Name = NULL,
  m2Name = NULL,
  colors = NULL,
  normalize = TRUE,
  yLims = NULL,
  borderCol = "gray",
  titleSize = 1,
  geneSize = 0.8,
  showPct = TRUE,
  pctSize = 0.7,
  axisSize = 0.8,
  legendTxtSize = 1
)

Arguments

m1	first MAF object
m2	second MAF object
genes	genes to be drawn. Default takes top 5 mutated genes.
orderBy	Order genes by mutation rate in 'm1' or 'm2'. Default 'NULL', keeps the same order of 'genes'
m1Name	optional name for first cohort
m2Name	optional name for second cohort
colors	named vector of colors for each Variant_Classification.
normalize	Default TRUE.
yLims	Default NULL. Auto estimates. Maximum values for 'm1' and 'm2' respectively
borderCol	Default gray
titleSize	Default 1
geneSize	Default 0.8
showPct	Default TRUE
pctSize	Default 0.7
axisSize	Default 0.8
legendTxtSize	Default 0.8

Details

Draws two barplots 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
coBarplot(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 0.380s elapsed (0.282s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.176s elapsed (0.128s cpu) 
null device 
          1 

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