rainfallPlot {maftools} | R Documentation |
Plots inter variant distance as a function of genomic locus.
rainfallPlot(maf, tsb = NULL, detectChangePoints = FALSE, ref.build = "hg19", color = NULL, savePlot = FALSE, width = 6, height = 3, fontSize = 12, pointSize = 1)
maf |
|
tsb |
specify sample names (Tumor_Sample_Barcodes) for which plotting has to be done. If NULL, draws plot for most mutated sample. |
detectChangePoints |
If TRUE, detectes genomic change points where potential kataegis are formed. Results are written to an output tab delimted file. |
ref.build |
Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19. |
color |
named vector of colors for each coversion class. |
savePlot |
If TRUE plot is saved to output pdf. Default FALSE. |
width |
width of plot to be saved. |
height |
height of plot to be saved. |
fontSize |
Default 12. |
pointSize |
Default 2. |
If 'detectChangePoints“ is set to TRUE, this method will use Change-Point detection method to identify genomic loci where average inter-mutation distance changes from the backgorund. Segments detected with less than 6 mutations are filtered out.
returns ggplot object of the plot which can be further modified. Results are written to an output file with suffix changePoints.tsv