track_narrow_peak {rGenomeTracks}R Documentation

Generate narrow peaks track

Description

Create genome_track object from narrow peak bed format.

Usage

track_narrow_peak(
  file,
  title = NULL,
  height = 3,
  overlay_previous = "no",
  orientation = NULL,
  line_width = 1,
  color = "#FF000080",
  max_value = NULL,
  show_data_range = TRUE,
  show_labels = TRUE,
  use_summit = TRUE,
  width_adjust = 1.5,
  type = "peak"
)

Arguments

file

String. The location of the track file

title

String. If specificed, the title of the track to be displayed.

height

Numeric. The height of the plotted track in cm. Default is 2. See notes.

overlay_previous

String. Options are "no" (default) or "yes" or "share-y".

orientation

String. Default is NULL. Other option is "inverted".

line_width

Numeric value for line width.

color

String. Hex color or string color. Default is "#1f78b4".

max_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

show_data_range

Boolean. Default is TRUE.

show_labels

Boolean. If TRUE, display labels on plotting which include peak tag, p-val and q-val.

use_summit

Boolean. If TRUE, peak summit data will be plotted.

width_adjust

Numeric value above 0 to adjust peaks' width. Default is 1.5.

type

String with options either "peak" or "box".

Details

narrowPeak file is bed file (4+3), where the 5th column is peak name, 6th column in p-value and 7th column in q-value. You might increase height it increased font size. narrowPeak format is very common with analysis pipelines involving MACS2. narrowPeak format provides the information of the peak summit. use_summit argument is used to deterimine if this information should be used. By default this information is used (use_summit = TRUE) although some peaks may look crooked. type argument specify if the plot will be:

Value

genome_track

Author(s)

Omar Elashkar

Examples

np_bed_dir <- system.file("extdata", "test2.narrowPeak", package = "rGenomeTracks")

tracks <-
  track_scalebar() +
  track_narrow_peak(np_bed_dir,
    title = "peak type with summit",
    height = 3,
    type = "peak",
    color = "green"
  ) +

  track_spacer(height = 2) +
  track_narrow_peak(np_bed_dir,
    title = "peak type without summit",
    height = 3,
    type = "peak",
    color = "green",
    use_summit = FALSE
  ) +
  track_spacer(height = 2) +
  track_narrow_peak(np_bed_dir,
    title = "Box type with summit",
    height = 3,
    type = "box",
    color = "blue"
  ) +
  track_spacer(height = 2) +
  track_narrow_peak(np_bed_dir,
    title = "Box type without summit",
    height = 3,
    type = "box",
    color = "blue",
    use_summit = FALSE
  ) +
  track_x_axis()
## Not run: 
plot_gtracks(tracks, chr = "X", start = 276 * 10^4, end = 280 * 10^4, trackLabelFraction = 0.2)

## End(Not run)

[Package rGenomeTracks version 0.99.8 Index]