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ChIP-style multi-track signal + peaks plot

Source: R/seq_chip.R
seq_chip.Rd

For each sample, seq_chip() stacks a seq_area() coverage track on top of an optional seq_bar() peak track, colouring both from the sample's colour. Tracks flow top-to-bottom (each one uses direction = "under"), so the returned SeqPlot is a single column of stacked tracks.

Usage

seq_chip(
  data,
  windows,
  sample_col = NULL,
  signal_col = NULL,
  peaks = NULL,
  peak_col = NULL,
  colors = NULL,
  scale_max = NULL,
  signal_height = 1,
  peak_height = 0.25,
  show_genes = NULL,
  track_id_prefix = "",
  legend = NULL,
  show_legend = TRUE,
  ...
)

Arguments

data

Either a named list of GRanges (one per sample), or a single GRanges with a sample column (pass its name via sample_col). Each signal GRanges must carry a numeric signal column (auto-detected).

windows

GRanges defining the view region.

sample_col

Column in data giving sample identity when data is a single GRanges. Ignored for list input.

signal_col

Explicit signal column name; auto-detected per sample when NULL.

peaks

Optional peak calls, mirroring data: either a named list of GRanges with the same names, or a single GRanges with sample_col.

peak_col

Optional column in peaks used for bar height; default renders uniform-height bars.

colors

Named character vector mapping sample name to colour. Defaults to cycling the flexoki_palette().

scale_max

Numeric scalar or named vector capping the signal y- axis per sample. NULL (default) autoscales.

signal_height

Relative height of each signal track.

peak_height

Relative height of each peak track.

show_genes

Optional GRanges for gene annotation — adds a final seq_gene() track beneath the sample tracks.

track_id_prefix

Prefix prepended to all auto-generated track_ids. Useful when composing multiple seq_chip() calls via seq_resolve().

legend

A LegendKey or SeqLegendSpec forwarded to each signal area element. NULL (default) produces no legend entry.

show_legend

Logical. When FALSE, signal area elements contribute no legend. Default TRUE.

...

Additional arguments forwarded to seq_track().

Value

A SeqPlot with per-sample signal (and optionally peak) tracks.

Examples

library(GenomicRanges)
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> 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, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
set.seed(1)
make_sig <- function() GRanges("chr1",
  IRanges(sort(sample(1:1e6, 200)), width = 500),
  score = rexp(200, rate = 0.2))
sigs <- list(S1 = make_sig(), S2 = make_sig())
seq_chip(sigs, windows = GRanges("chr1", IRanges(1, 1e6)))