lollipopPlot2 {maftools}R Documentation

Compare two lollipop plots

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, axisTextSize = c(1, 1),
  pointSize = 1.2, domainLabelSize = 1, legendTxtSize = 1)

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.

axisTextSize

text size for axis labels. Default 1.

pointSize

size of lollipop heads. Default 1.2

domainLabelSize

text size for domain labels. Default 1.

legendTxtSize

Default 1.

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")

[Package maftools version 2.0.16 Index]