Computes and plot the cosine similarity of each individual signature is computed against each COSMIC signature from COMIC V3.2

This function computes and plot the cosine similarity of each individual signature is computed against each COSMIC signature from COMIC V3.2. The cosine similarity is a value between 0 (distinct) and 1 (identical) and indicates how much two vectors are alike.

generateCOSMICMutSigSimHeatmap(
  mymaf,
  use_silent_mutations = FALSE,
  full_output = FALSE,
  show_broad_categories = TRUE,
  clin_data = NULL,
  clin_data_colors = NULL,
  add_sample_names = NULL,
  savename = NULL,
  fig_height = NULL,
  fig_width = NULL
)

Arguments

mymaf

mutation count matrix (dimensions: a mutation features X n samples)

use_silent_mutations

96 mutation count matrix (dimensions: a mutation features X m samples)

full_output

return full output including the etiology matrix and plot data

show_broad_categories

To show broad etiology categories

clin_data

Clinical data to be plotted in the heatmap

clin_data_colors

Clinical data colors

add_sample_names

Whether or not to add column labels; if set to NULL, will add labels only if # samples less than 10

savename

file name of the plot

fig_height

Output height (inches); set to NULL to size automatically; only used if savename is set.

fig_width

Output width (inches); set to NULL to size automatically; only used if savename is set.

Value

Complex Heatmap object. If full_output is TRUE it will consist of a list including heatmap object, etiology matrix and plot data.

Examples

library(MAFDash)
library(maftools)
library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.6.2
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite:
#> Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>   genomic data. Bioinformatics 2016.
#> 
#> This message can be suppressed by:
#>   suppressPackageStartupMessages(library(ComplexHeatmap))
#> ========================================
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
val<-generateCOSMICMutSigSimHeatmap(read.maf(maf));draw(val)
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.244s elapsed (0.220s cpu) 
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:base’:
#> 
#>     expand.grid
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> -Extracting 5' and 3' adjacent bases
#> -Extracting +/- 20bp around mutated bases for background C>T estimation
#> -Estimating APOBEC enrichment scores
#> --Performing one-way Fisher's test for APOBEC enrichment
#> ---APOBEC related mutations are enriched in  12.658 % of samples (APOBEC enrichment score > 2 ;  10  of  79  samples)
#> -Creating mutation matrix
#> --matrix of dimension 80x96