Breakpoint Associated Heatmaps

This function generates a heatmap of the specified pattern, over breakpoints aligned at the centre of the plot. The result can be piped into heatmaps::smoothHeatmap and then heatmaps::plotHeatmapList or heatmaps::plotHeatmapMeta

Usage

bp_heatmap(gr, window, pattern, ...)

Arguments

gr

GRanges object containing pairwise alignment

window

Range over which heatmap characteristic is plotted. Breakpoints will be aligned at the center of this.

pattern

Character string of desired pattern/characteristic to be plotted on heatmap.

...

Pass other arguments to get_bps.

Value

Returns a Heatmap object of pattern around centred breakpoints.

Note

The GRanges object is expected to have a sequence information (see seqinfo) that allows the retrieval its corresponding BSgenome object via the BSgenome::getBSgenome function.

See also

Other plot functions: bp_pair_analysis(), feature_coverage(), makeOxfordPlots(), plotApairOfChrs()

Other heatmap functions: bp_pair_analysis(), feature_coverage()

Author

Charlotte West

Charles Plessy

Examples

# The plot makes no sense, but that is the best example I have at the moment.
exdata_Sac <- system.file("extdata/SacCer3__SacPar.gff3.gz", package = "GenomicBreaks")
gb <- load_genomic_breaks(exdata_Sac, BSgenome.Scerevisiae.UCSC.sacCer3::Scerevisiae)
bp_heatmap(gb, 200, 'GC', dir = "left") |>
  heatmaps::smoothHeatmap() |> heatmaps::plotHeatmapList()
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:GenomicBreaks’:
#> 
#>     pairwiseAlignment
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> 
#> Attaching package: ‘rtracklayer’
#> The following object is masked from ‘package:BiocIO’:
#> 
#>     FileForFormat
#> 
#> Calculating kernel density...
#> plotting heatmap GC