Description Usage Arguments Value See Also Examples
View source: R/plotOncodriveClust.R
Takes results from oncodrive
and plots them as a scatter plot. Size of the gene shows number of clusters (hotspots), x-axis can either be an absolute number of variants
accumulated in these clusters or a fraction of total variants found in these clusters. y-axis is fdr values transformed into -log10 for better representation. Labels indicate Gene name with number clusters
observed.
1 2 3 4 5 6 7 8 | plotOncodrive(
res = NULL,
fdrCutOff = 0.05,
useFraction = FALSE,
colCode = NULL,
bubbleSize = 1,
labelSize = 1
)
|
res |
results from |
fdrCutOff |
fdr cutoff to call a gene as a driver. |
useFraction |
if TRUE uses a fraction of total variants as X-axis scale instead of absolute counts. |
colCode |
Colors to use for indicating significant and non-signififcant genes. Default NULL |
bubbleSize |
Size for bubbles. Default 2. |
labelSize |
font size for labelling genes. Default 1. |
Nothing
1 2 3 4 | laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.sig <- oncodrive(maf = laml, AACol = 'Protein_Change', minMut = 5)
plotOncodrive(res = laml.sig, fdrCutOff = 0.1)
|
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