plotStories: plots line plots of clonalities

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

plots line plots of clonalities

Description

plots line plots of clonalities

Usage

plotStories(
  stories,
  variants,
  col = "default",
  lty = "default",
  add = F,
  alpha = 1,
  xlab = "sample",
  ylab = "clonality",
  lwd = "default",
  errorBars = T,
  setPar = T,
  legend = T,
  labels = T,
  xlim = "default",
  genome = "hg19",
  xSpread = 0.25,
  sampleOrder = NA,
  annotationMethod = "VariantAnnotation",
  ...
)

Arguments

stories	dataFrame from superFreq. such as data$stories$stories$mySample$all.
variants	dataFrame from superFreq. such as data$allVariants$variants$variants$mySample
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.
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'
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.
setPar	logical. If the margins are set. Default TRUE.
legend	logical. If a legend is plotted. Default TRUE.
labels	logical. If labels are plotted. Default TRUE.
xlim	numerical. The X limits. Default "default' set it depending on number of samples and clones.
genome	character. The genome the sample is aligned to. 'hg19', 'hg38' or 'mm10'
xSpread	numerical. The stread of the points over a sample. Default 0.25.
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.

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.