Creates a set of plot summarising a mutation file.

Usage

mutation_viz(mutation, ...)

Arguments

mutation: Raw mutation dataframe containing alteration data
...: any argument belonging to the gene_binary method

Value

Returns a list of the following plots:

varclass Barplot of counts of each variant classification

vartype Barplot of counts of each variant type

snvclass Histogram of counts of each SNV class

samplevar Histogram of counts variants per patient

topgenes Barplot of counts of top variant genes

genecor Correlation heatmap of the top 10 genes

Examples

mutation_viz(gnomeR::mutations)
#> ! `samples` argument is `NULL`. We will infer your cohort inclusion and resulting data frame will include all samples with at least one alteration in mutation, fusion or cna data frames
#> ! 7 mutations have `NA` or blank in the mutation_status column instead of 'SOMATIC' or 'GERMLINE'. These were assumed to be 'SOMATIC' and were retained in the resulting binary matrix.
#> $varclass

#> 
#> $vartype

#> 
#> $samplevar

#> 
#> $topgenes

#> 
#> $genecor

#>