maftools (version 0.99.30)

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

Description

Draws lollipop plot of amino acid changes.

Usage

lollipopPlot(maf, gene = NULL, refSeqID = NULL, proteinID = NULL,
  labelPos = NULL, AACol = NULL, repel = FALSE, colors = NULL)

Arguments

maf

an MAF object generated by read.maf

gene

HGNC symbol for which protein structure to be drawn.

refSeqID

RefSeq transcript identifier for gene if known.

proteinID

RefSeq protein identifier for gene if known.

labelPos

Amino acid positions to label. If 'all', labels all variants.

AACol

manually specify column name for amino acid changes. Default looks for field 'AAChange'

repel

If points are too close to each other, use this option to repel them. Default FALSE.

colors

named vector of colors for each Variant_Classification. Default NULL.

Value

ggplot object of the plot, which can be futher modified.

Details

This function by default looks for field "AAChange" in maf file. One can also manually specify field name containing amino acid changes.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
lollipopPlot(maf = laml, gene = 'KIT', AACol = 'Protein_Change')

# }