Skip to contents

Copy-number scatter plot

Source: R/seq_copynumber.R
seq_copynumber.Rd

Builds a seq_plot() with one track showing per-bin copy-number data: a scatter of continuous ratio / log-ratio values, coloured by integer CN state. Optional dotted reference lines mark integer CN values present in the data, and an optional segmentation overlay draws a horizontal line segment for each called segment.

Usage

seq_copynumber(
  data,
  windows,
  cn_col = NULL,
  ratio_col = NULL,
  state_colors = NULL,
  segment_data = NULL,
  segment_col = NULL,
  show_reference_lines = TRUE,
  reference_line_col = "grey50",
  track_height = 1,
  track_id = NULL,
  legend = NULL,
  show_legend = TRUE,
  ...
)

Arguments

data

A GRanges with one row per bin and mcols columns for the CN state and the continuous ratio.

windows

A GRanges of genomic windows defining the view.

cn_col

Name of the mcols column giving integer CN state. Auto- detected when NULL.

ratio_col

Name of the mcols column giving the continuous ratio / log-ratio. Auto-detected when NULL.

state_colors

Named character vector keyed by CN state (as a string). Defaults to a diverging blue -> grey -> orange palette.

segment_data

Optional GRanges of segmentation calls. Drawn as horizontal line segments over the scatter.

segment_col

Column in segment_data giving the per-segment y value (e.g. segment mean). Auto-detected from the same candidates as ratio_col when NULL.

show_reference_lines

Logical; draw dotted horizontal lines at each integer CN value present in the data range. Default TRUE.

reference_line_col

Colour for the reference lines.

track_height

Relative track height.

track_id

Character track_id for the generated track. Defaults to "copynumber".

legend

A LegendKey or SeqLegendSpec attached to the scatter element. NULL (default) produces no legend entry.

show_legend

Logical. When FALSE, the scatter element contributes no legend. Default TRUE.

...

Additional arguments forwarded to seq_track().

Value

A SeqPlot object composable via %+%, %|%, %__%, and seq_resolve().

Details

The CN state and ratio column names are auto-detected when not specified. For CN state the search order is c("cn", "copy_number", "CN", "state", "integer_cn"); for ratio it is c("log2ratio", "logR", "log2R", "ratio", "log2_ratio"). When no match is found the first integer / numeric column is used with a warning.

Examples

library(GenomicRanges)
gr <- GRanges("chr1", IRanges(seq(1, 1e6, by = 1e4), width = 5000),
              cn        = sample(0:4, 100, replace = TRUE),
              log2ratio = rnorm(100, 0, 0.3))
win <- GRanges("chr1", IRanges(1, 1e6))
seq_copynumber(gr, windows = win)
#> 4 out-of-bounds data points excluded! (seq_segment)