qualityScatter: plots a scatter of the VAF between two samples

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

plots a scatter of the VAF between two samples

Description

plots a scatter of the VAF between two samples

Usage

qualityScatter(
  q1,
  q2,
  ps = NA,
  covScale = 100,
  maxCex = 1.5,
  minCov = 10,
  main = "",
  xlab = "variant frequency: sample1",
  ylab = "variant frequency: sample2",
  plotFlagged = T,
  cpus = 1,
  verbose = T,
  print = F,
  printRedCut = 0.99,
  printOnlyNovel = F,
  plotPosition = F,
  genome = "hg19",
  xlim = c(0, 1),
  ylim = c(0, 1),
  outputHighlighted = F,
  frame.plot = F,
  legend = T,
  redCut = 0.75,
  forceCol = NA,
  add = F,
  GoI = c(),
  printCex = 1,
  doPlot = T,
  minSomaticP = 0,
  ignoreFlagsInOne = c("Svr", "Mv", "Nab"),
  ignoreFlagsInBoth = c("Srr"),
  flagOpacity = 0.4,
  severityWidth = 0.5,
  cosmicWidth = 3,
  ...
)

Arguments

q1	data.frame. The variants of the x sample, taken from the loaded data$allVariants$variants$variants$mySample
q2	data.frame. The variants of the y sample, taken from the loaded data$allVariants$variants$variants$mySample
ps	numeric. p-values of the variants. Default NA calculates them, but supplying them directly can save time.
covScale	numeric. The coverage where the point size is one. Larger coverage scale will make the points smaller. Default 100.
maxCex	numeric. Cutoff for maximum point size. Default 1.5.
minCov	numeric. Variants with coverage below this level are not plotted.
plotFlagged	logical. If flagged variants shouldbe plotted. Default T.
cpus	numeric. The maximum number of cpus to run on.
verbose	logical. If some diagnostic outputs should be printed to terminal. Default T.
print	logical. If gene names of significantly different VAFs should be printed on the plot. Default F.
printRedCut	numeric. The redness (0 to 1) above which gene names are printed if print is TRUE. Default 0.99.
printOnlyNovel	logical. Only print gene names if the VAF is small in one sample if print is TRUE. Default FALSE.
plotPosition	logical. Show the genomic position of each variant with a thin line to the top of the plot, as well as colour coding. Default FALSE.
genome	character. The genome aligned to. Default 'hg19'.
outputHighlighted	logical. Prints the printed genes to terminal. Default FALSE.
legend	logical. If the legend should be included. Default TRUE.
redCut	numeric. Sets how significantly different the VAFs have to be fo the dot to be coloured red. Default 0.75.
forceCol	colour. Forces all the dots to this colour. Default NA does colour by significance.
add	logical. If TRUE, the dots are added to the existing plot. Default FALSE.
GoI	character. vector of genes of interest that always get their gene name printed on the plot. Default c().
printCex	numeric. A scaling factor for the size of the printed gene names. Default 1.
doPlot	numeric. If FALSE, the plot isn't made, but p values are returned. Default TRUE.
minSomaticP	numeric. Variants with a somaticP below this cut in both samples are excluded. Default 0 includes all points.
ignoreFlagsInOne	character. Variants with this flag in one (but not both) sample are plotted even if plotFlagged is FALSE. Default c('Svr', 'Mv', 'Nab').
ignoreFlagsInBoth	character. Variants with this flag are plotted even if plotFlagged is FALSE. Default c('Srr').
flagOpacity	numeric. The opacity of the flagged variants. Default 0.4.
severityWidth	numeric. A scaling factor for the size of the orange circle for protein altering SNVs. Default 0.5.
cosmicWidth	numeric. A scaling factor for the size of the green circle around COSMIC census genes. Default 3.
...	remaining arguments are passed to plot(...)

Details

Deprecated. Use superFreq::vafScatter instead.

Examples

#random matrix to plot, centered around 0. Plot in 'DE' colours.
mx = matrix(rt(400, df=10), nrow=100)
makeHeatmap(mx, col='DE')

#random matrix to plot, between 0 and 1. Plot in default and sunset colours.
mx = matrix(runif(400), nrow=100)
makeHeatmap(mx)
makeHeatmap(mx, col='sunset')

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.