Description Usage Arguments Value Examples
plotMutChange
Function to plot frequency of mutation changes.
1 2 3 4 |
sample.mutations |
data frame in MAF like format.
Columns (with exactly same names) which
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silent |
a boolean value indicating should silent mutations be counted. By default it is True. |
fill |
a boolean value indicating should plot only represent proportion between 3 types of mutations, not counts. By default it is True |
Tumor_Sample_Barcode |
(optional) integer/numeric value indicating column in |
Variant_Type |
(optional) integer/numeric value indicating column in |
Variant_Classification |
(optional) integer/numeric value indicating column in |
Reference_Allele |
(optional) integer/numeric value indicating column in |
Tumor_Seq_Allele2 |
(optional) integer/numeric value indicating column in |
ggplot2 object
1 2 3 4 | # plot SNVs changes patterns
plotMutChange(sample.genes.mutect)
# plot SNVs changes patterns only for non silent mutaions
plotMutChange(sample.genes.mutect, silent=FALSE, fill=FALSE)
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