lollipopPlot2: Compare two lollipop plots

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Compare two lollipop plots

Usage

lollipopPlot2(
  m1,
  m2,
  gene = NULL,
  AACol1 = NULL,
  AACol2 = NULL,
  m1_name = NULL,
  m2_name = NULL,
  m1_label = NULL,
  m2_label = NULL,
  refSeqID = NULL,
  proteinID = NULL,
  labPosAngle = 0,
  labPosSize = 0.9,
  colors = NULL,
  alpha = 1,
  axisTextSize = c(1, 1),
  pointSize = 1.2,
  roundedRect = TRUE,
  showDomainLabel = TRUE,
  domainBorderCol = "black",
  domainLabelSize = 1,
  legendTxtSize = 1,
  verbose = TRUE
)

Arguments

m1	first MAF object
m2	second MAF object
gene	HGNC symbol for which protein structure to be drawn.
AACol1	manually specify column name for amino acid changes in m1. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'.
AACol2	manually specify column name for amino acid changes in m2. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'.
m1_name	name for m1 cohort. optional.
m2_name	name for m2 cohort. optional.
m1_label	Amino acid positions to label for m1 cohort. If 'all', labels all variants.
m2_label	Amino acid positions to label for m2 cohort. If 'all', labels all variants.
refSeqID	RefSeq transcript identifier for gene if known.
proteinID	RefSeq protein identifier for gene if known.
labPosAngle	angle for labels. Defaults to horizonal 0 degree labels. Set to 90 for vertical; 45 for diagonal labels.
labPosSize	Text size for labels. Default 3
colors	named vector of colors for each Variant_Classification. Default NULL.
alpha	color adjustment. Default 1
axisTextSize	text size for axis labels. Default 1.
pointSize	size of lollipop heads. Default 1.2
roundedRect	Default FALSE. If 'TRUE' domains are drawn with rounded corners. Requires berryFunctions
showDomainLabel	Label domains within the plot. Default TRUE. If FALSE domains are annotated in legend.
domainBorderCol	Default "black". Set to NA to remove.
domainLabelSize	text size for domain labels. Default 1.
legendTxtSize	Default 1.
verbose	Default TRUE

Details

Draws lollipop plot for a gene from two cohorts

See Also

lollipopPlot

mafCompare

Examples

primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
primary.apl <- read.maf(maf = primary.apl)
relapse.apl <- read.maf(maf = relapse.apl)
lollipopPlot2(m1 = primary.apl, m2 = relapse.apl, gene = "FLT3",AACol1 = "amino_acid_change", AACol2 = "amino_acid_change", m1_name = "Primary", m2_name = "Relapse")

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 0.310s elapsed (0.269s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.160s elapsed (0.144s cpu) 
Gene: FLT3

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