lollipopPlot2: Compare two lollipop plots
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

lollipopPlot2

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,
  alpha = 1,
  axisTextSize = c(1, 1),
  pointSize = 1.2,
  roundedRect = TRUE,
  showDomainLabel = TRUE,
  domainBorderCol = "black",
  domainLabelSize = 1,
  legendTxtSize = 1,
  verbose = TRUE
)

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.
`alpha`	color adjustment. Default 1
`axisTextSize`	text size for axis labels. Default 1.
`pointSize`	size of lollipop heads. Default 1.2
`roundedRect`	Default FALSE. If 'TRUE' domains are drawn with rounded corners. Requires `berryFunctions`
`showDomainLabel`	Label domains within the plot. Default TRUE. If FALSE domains are annotated in legend.
`domainBorderCol`	Default "black". Set to NA to remove.
`domainLabelSize`	text size for domain labels. Default 1.
`legendTxtSize`	Default 1.
`verbose`	Default TRUE

Details

Draws lollipop plot for a gene from two cohorts

Value

invisible list of domain overlaps

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")

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