lollipopPlot: Draws lollipop plot of amino acid changes on to Protein...
In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Details Value Examples

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

lollipopPlot(
  maf,
  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
)

`maf`	an `MAF` object generated by `read.maf`
`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

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.

Nothing

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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')