ggMutDens {BiocOncoTK} | R Documentation

## make a ggplot with density traces of mutations per base pair, for 'most mutated' tumor types in a given interval

### Description

make a ggplot with density traces of mutations per base pair, for 'most mutated' tumor types in a given interval

### Usage

    ggMutDens(
      bq,
      basicfilt = function(data) dplyr::filter(data, Consequence ==
        "non_coding_transcript_exon_variant"),
      chrname = "15",
      start = 20450000,
      end = 20730000,
      project_volume = 5,
      maxnrec = 50000,
      binwidth = 5000,
      xlab.in = " "
    )

### Arguments

`bq` | bigrquery BigQueryConnection instance
`basicfilt` | a dplyr::filter operation, defaulting to select non-coding variants in mc3 MAF
`chrname` | character(1) chromosome token in NCBI seqlevels style
`start` | numeric(1) base coordinate to start
`end` | numeric(1) base coordinate to end
`project_volume` | numeric(1) tumor types will have different numbers of contributions; this parameter tells how many tumor types to represent, counting down from the most frequently represented
`maxnrec` | numeric(1) for as.data.frame
`binwidth` | numeric(1) passed to geom_freqpoly
`xlab.in` | character(1) passed to ggplot2::xlab

### Value

instance of ggplot

### Examples

    if (interactive()) {
     if (!requireNamespace("ggplot2")) stop("install ggplot2 to run this function")
     bq = try(pancan_BQ())
     if (!inherits(bq, "try-error")) {
      ggMutDens(bq)
      }
     }

[Package BiocOncoTK version 1.12.1 Index]