plot_96_profile: Plot 96 trinucleotide profile

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description

Plot relative contribution of 96 trinucleotides

Usage

plot_96_profile(mut_matrix, colors = NA, ymax = 0.2, condensed = FALSE)

Arguments

mut_matrix	96 trinucleotide profile matrix
colors	Optional 6 value color vector.
ymax	Y axis maximum value, default = 0.2
condensed	More condensed plotting format. Default = F.

Value

96 trinucleotide profile plot

See Also

mut_matrix, plot_profile_heatmap, plot_river

Examples

## See the 'mut_matrix()' example for how we obtained the
## mutation matrix information:
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
  package = "MutationalPatterns"
))

## Plot the 96-profile of three samples
plot_96_profile(mut_mat[, c(1, 4, 7)])

## Plot a condensed profile
plot_96_profile(mut_mat[, c(1, 4, 7)], condensed = TRUE)

## It's also possible to plot signatures, for example signatures
## generated with NMF
## See 'extract_signatures()' on how we obtained these signatures.
nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
  package = "MutationalPatterns"
))

## Optionally, provide signature names
colnames(nmf_res$signatures) <- c("Signature A", "Signature B")

## Generate the plot
plot_96_profile(nmf_res$signatures)

Example output

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

The following object is masked from ‘package:S4Vectors’:

    new2

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 1/1

Attaching package: ‘NMF’

The following object is masked from ‘package:S4Vectors’:

    nrun

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.