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

View source: R/lollipopPlot.R

lollipopPlotR Documentation

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 'FALSEā€œ 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 March 26, 2024, 11:13 a.m.