plots a scatter of the VAF between two samples
vafScatter(q1, q2, ps = NA, covScale = 100, maxCex = 1.5,
minCov = 10, main = "", xlab = "variant frequency: sample1",
ylab = "variant frequency: sample2", plotFlagged = T, cpus = 1,
verbose = T, print = F, printRedCut = 0.99, printOnlyNovel = F,
plotPosition = F, genome = "hg19", xlim = c(0, 1), ylim = c(0,
1), outputHighlighted = F, frame.plot = F, legend = T,
redCut = 0.75, forceCol = NA, add = F, GoI = c(), printCex = 1,
doPlot = T, minSomaticP = 0, ignoreFlagsInOne = c("Svr", "Mv",
"Nab"), ignoreFlagsInBoth = c("Srr"), flagOpacity = 0.4,
severityWidth = 0.5, cosmicWidth = 3, ...)data.frame. The variants of the x sample, taken from the loaded data$allVariants$variants$variants$mySample
data.frame. The variants of the y sample, taken from the loaded data$allVariants$variants$variants$mySample
numeric. p-values of the variants. Default NA calculates them, but supplying them directly can save time.
numeric. The coverage where the point size is one. Larger coverage scale will make the points smaller. Default 100.
numeric. Cutoff for maximum point size. Default 1.5.
numeric. Variants with coverage below this level are not plotted.
logical. If flagged variants shouldbe plotted. Default T.
numeric. The maximum number of cpus to run on.
logical. If some diagnostic outputs should be printed to terminal. Default T.
logical. If gene names of significantly different VAFs should be printed on the plot. Default F.
numeric. The redness (0 to 1) above which gene names are printed if print is TRUE. Default 0.99.
logical. Only print gene names if the VAF is small in one sample if print is TRUE. Default FALSE.
logical. Show the genomic position of each variant with a thin line to the top of the plot, as well as colour coding. Default FALSE.
character. The genome aligned to. Default 'hg19'.
logical. Prints the printed genes to terminal. Default FALSE.
logical. If the legend should be included. Default TRUE.
numeric. Sets how significantly different the VAFs have to be fo the dot to be coloured red. Default 0.75.
colour. Forces all the dots to this colour. Default NA does colour by significance.
logical. If TRUE, the dots are added to the existing plot. Default FALSE.
character. vector of genes of interest that always get their gene name printed on the plot. Default c().
numeric. A scaling factor for the size of the printed gene names. Default 1.
numeric. If FALSE, the plot isn't made, but p values are returned. Default TRUE.
numeric. Variants with a somaticP below this cut in both samples are excluded. Default 0 includes all points.
character. Variants with this flag in one (but not both) sample are plotted even if plotFlagged is FALSE. Default c('Svr', 'Mv', 'Nab').
character. Variants with this flag are plotted even if plotFlagged is FALSE. Default c('Srr').
numeric. The opacity of the flagged variants. Default 0.4.
numeric. A scaling factor for the size of the orange circle for protein altering SNVs. Default 0.5.
numeric. A scaling factor for the size of the green circle around COSMIC census genes. Default 3.
remaining arguments are passed to plot(...)
This function takes two superFreq data frames of variants, and scatters the VAFs against each other.