lollipopPlot: Draws lollipop plot of amino acid changes on to Protein...

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Draws lollipop plot of amino acid changes on to Protein structure.

Description

Draws lollipop plot of amino acid changes. Protein domains are derived from PFAM database.

Usage

lollipopPlot(
  maf,
  data = NULL,
  gene = NULL,
  AACol = NULL,
  labelPos = NULL,
  labPosSize = 0.9,
  showMutationRate = TRUE,
  showDomainLabel = TRUE,
  cBioPortal = FALSE,
  refSeqID = NULL,
  proteinID = NULL,
  roundedRect = TRUE,
  repel = FALSE,
  collapsePosLabel = TRUE,
  showLegend = TRUE,
  legendTxtSize = 0.8,
  labPosAngle = 0,
  domainLabelSize = 0.8,
  axisTextSize = c(1, 1),
  printCount = FALSE,
  colors = NULL,
  domainAlpha = 1,
  domainBorderCol = "black",
  bgBorderCol = "black",
  labelOnlyUniqueDoamins = TRUE,
  defaultYaxis = FALSE,
  titleSize = c(1.2, 1),
  pointSize = 1.5
)

Arguments

maf	an MAF object generated by read.maf
data	Provide a custom two column data frame with pos and counts instead of an MAF. Input data can also contain an additional column 'Variant_Classification' used for color coding the dots.
gene	HGNC symbol for which protein structure to be drawn.
AACol	manually specify column name for amino acid changes. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'. Changes can be of any format i.e, can be a numeric value or HGVSp annotations (e.g; p.P459L, p.L2195Pfs*30 or p.Leu2195ProfsTer30)
labelPos	Amino acid positions to label. If 'all', labels all variants.
labPosSize	Text size for labels. Default 0.9
showMutationRate	Whether to show the somatic mutation rate on the title. Default TRUE
showDomainLabel	Label domains within the plot. Default TRUE. If 'FALSE“ domains are annotated in legend.
cBioPortal	Adds annotations similar to cBioPortals MutationMapper and collapse Variants into Truncating and rest.
refSeqID	RefSeq transcript identifier for gene if known.
proteinID	RefSeq protein identifier for gene if known.
roundedRect	Default TRUE. If 'TRUE' domains are drawn with rounded corners. Requires berryFunctions
repel	If points are too close to each other, use this option to repel them. Default FALSE. Warning: naive method, might make plot ugly in case of too many variants!
collapsePosLabel	Collapses overlapping labels at same position. Default TRUE
showLegend	Default TRUE
legendTxtSize	Text size for legend. Default 0.8
labPosAngle	angle for labels. Defaults to horizonal 0 degree labels. Set to 90 for vertical; 45 for diagonal labels.
domainLabelSize	text size for domain labels. Default 0.8
axisTextSize	text size x and y tick labels. Default c(1,1).
printCount	If TRUE, prints number of summarized variants for the given protein.
colors	named vector of colors for each Variant_Classification. Default NULL.
domainAlpha	Default 1
domainBorderCol	Default "black". Set to NA to remove.
bgBorderCol	Default "black". Set to NA to remove.
labelOnlyUniqueDoamins	Default TRUE only labels unique doamins.
defaultYaxis	If FALSE, just labels min and maximum y values on y axis.
titleSize	font size for title and subtitle. Default c(1.2, 1)
pointSize	size of lollipop heads. Default 1.5

Details

This function by default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change' in maf file. One can also manually specify field name containing amino acid changes.

Value

Nothing

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
lollipopPlot(maf = laml, gene = 'KIT', AACol = 'Protein_Change')

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