BigwigTrack: Plot data from BigWig

Description Usage Arguments

View source: R/visualization.R

Description

Create a BigWig track. Note that this function does not work on windows.

Usage

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BigwigTrack(
  region,
  bigwig,
  smooth = 200,
  type = "coverage",
  y_label = "Score",
  max.downsample = 3000,
  downsample.rate = 0.1
)

Arguments

region

GRanges object specifying region to plot

bigwig

Path to a bigwig file

smooth

Number of bases to smooth data over (rolling mean). If NULL, do not apply smoothing.

type

Plot type. Can be one of "line", "heatmap", or "coverage"

y_label

Y-axis label

max.downsample

Minimum number of positions kept when downsampling. Downsampling rate is adaptive to the window size, but this parameter will set the minimum possible number of positions to include so that plots do not become too sparse when the window size is small.

downsample.rate

Fraction of positions to retain when downsampling. Retaining more positions can give a higher-resolution plot but can make the number of points large, resulting in larger file sizes when saving the plot and a longer period of time needed to draw the plot.


timoast/signac documentation built on Dec. 14, 2021, 11:34 p.m.