build_pile_plot: Build a multi-track pileup plot

Description Usage Arguments Value

View source: R/plotting_functions.R

Description

Build a multi-track pileup plot

Usage

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build_pile_plot(gr_list, ucsc_loc, highlight_loc = NULL,
  padding = c(1e+05, 1e+05), gr_groups = NULL, group_colors = NULL,
  norm = c("PM", "max"), max_val = NULL, window_size = NULL,
  window_mode = c("max", "mean", "median"), target_color = "#B7B7B7",
  highlight_color = "#F9ED32")

Arguments

gr_list

A list of GRanges objects

ucsc_loc

A target location, in UCSC format (e.g. "chr1:533,235-552,687)

highlight_loc

A location to use for highlights in UCSC format

padding

A 2-element numeric vector with upstream and downstream padding around the ucsc_loc to extend the plotting window.

gr_groups

A vector indicating which group each GRanges object in gr_list belongs to. If NULL, will group all samples into a single track.

group_colors

A named vector, one per group, with colors for each group. Names should match values in gr_groups.

norm

Normalization for each group. Currently support is per-million ("PM") and "max".

max_val

A maximum value to use for scaling the y-values in each track.

window_size

Window bin size to use for region down-sampling. If NULL, will not downsample.

window_mode

If using window_size, what value to use for each window. Options are "max","mean", and "median".

target_color

The color of the background rectangle to highlight the region in ucsc_loc.

highlight_color

The color the background rectangle to highlight the region in highlight_loc.

Value

A ggplot2 plot object


AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.