View source: R/makeRiverPlots.R
plotRiver | R Documentation |
plots a river plot
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,
...
)
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. |
This function plots the story lines from a superFreq analysis. Can be used both for individual mutations or for clones.
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