plotRiver: plots a river plot

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

plots a river plot

Description

plots a river plot

Usage

plotRiver(
  cloneTree,
  cloneStories,
  storyList,
  allStories,
  variants,
  genome = "hg19",
  normalise = T,
  xlim = "default",
  ylim = "default",
  labels = T,
  setPar = T,
  sampleOrder = "default",
  excludeClones = c(),
  markDodgy = T,
  colourPool = c(),
  ignoreStoriesBelowSigma = 2,
  smallPlot = F,
  annotationMethod = "VariantAnnotation",
  plotSampleNames = T,
  ...
)

Arguments

variants	dataFrame from superFreq. such as data$allVariants$variants$variants$mySample
genome	character. The genome the sample is aligned to. 'hg19', 'hg38' or 'mm10'
xlim	numerical. The X limits. Default "default' set it depending on number of samples and clones.
labels	logical. If labels are plotted. Default TRUE.
setPar	logical. If the margins are set. Default TRUE.
sampleOrder	character. The order of the samples. Default NA retains the order in the input.
...	remaining arguments are passed to base plot(...) if add=F, otherwise ignored.
stories	dataFrame from superFreq. such as data$stories$stories$mySample$all.
col	colour. The colour of the lines. Default 'default' sets different colours on all lines.
lty	linetype. The line type of the lines. Default 'default' sets different line types on all lines.
lwd	linetype. The line width of the lines. Default 'default' sets different line width from accuracy.
errorBars	logical. If error bars are used. Default TRUE.
add	logical. If the data should be plotted on top of whatever is already there. Default FALSE.
alpha	numerical. A opaqueness multiplier. Default 1.
xlab	character. The X label. Default "sample'
ylab	character. The Y label. Default "clonality'
legend	logical. If a legend is plotted. Default TRUE.
xSpread	numerical. The stread of the points over a sample. Default 0.25.

Details

This function plots the story lines from a superFreq analysis. Can be used both for individual mutations or for clones.

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