plots line plots of clonalities
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", ...)dataFrame from superFreq. such as data$stories$stories$mySample$all.
dataFrame from superFreq. such as data$allVariants$variants$variants$mySample
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.
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'
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 margins are set. Default TRUE.
logical. If a legend is plotted. Default TRUE.
logical. If labels are plotted. Default TRUE.
numerical. The X limits. Default "default' set it depending on number of samples and clones.
character. The genome the sample is aligned to. 'hg19', 'hg38' or 'mm10'
numerical. The stread of the points over a sample. Default 0.25.
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.
This function plots the story lines from a superFreq analysis. Can be used both for individual mutations or for clones.