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, ...)dataFrame from superFreq. such as data$allVariants$variants$variants$mySample
character. The genome the sample is aligned to. 'hg19', 'hg38' or 'mm10'
numerical. The X limits. Default "default' set it depending on number of samples and clones.
logical. If labels are plotted. Default TRUE.
logical. If the margins are set. Default TRUE.
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.
dataFrame from superFreq. such as data$stories$stories$mySample$all.
colour. The colour of the lines. Default 'default' sets different colours on all lines.
linetype. The line type of the lines. Default 'default' sets different line types on all lines.
linetype. The line width of the lines. Default 'default' sets different line width from accuracy.
logical. If error bars are used. Default TRUE.
logical. If the data should be plotted on top of whatever is already there. Default FALSE.
numerical. A opaqueness multiplier. Default 1.
character. The X label. Default "sample'
character. The Y label. Default "clonality'
logical. If a legend is plotted. Default TRUE.
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.