lollipopPlot2: Compare two lollipop plots

Description Usage Arguments Details See Also Examples

View source: R/lollipopPlot2.R

Description

Compare two lollipop plots

Usage

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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

See Also

lollipopPlot

mafCompare

Examples

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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")

Example output

-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 45 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.310s elapsed (0.269s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.160s elapsed (0.144s cpu) 
Gene: FLT3

maftools documentation built on Feb. 6, 2021, 2 a.m.