set_track_parameters: set_track_parameters

In skummerf/GenomicWidgets: interactive visualization of genomics data

Description

Setup parameters for plotting coverage signals along genome tracks. Result from this function can be passed to plot_tracks

Usage

## S4 method for signature 'character'
set_track_parameters(object, annotation = NULL,
  track_names = if (!is.null(names(object))) names(object) else
  basename(object), groups = track_names, share_y = TRUE,
  showlegend = TRUE, colors = NULL, fill = c("tozeroy", "none"),
  mode = "lines", annotation_position = c("bottom", "top"),
  annotation_size = 0.25, summary = NULL, layout = list())

Arguments

object	vector of bam or bigwig file names
annotation	TxDb or OrganismDb object
track_names	names to associate with each file
groups	vector of group assignments. traces will be grouped onto subplots based on group assignments (if only showing 1 region)
share_y	share the y axis?
showlegend	show the legend?
colors	colors for each bam file
fill	fillmode for line plot
mode	mode for plot
annotation_position	plot annotations on bottom or on top of signal traces
annotation_size	relative size of annotation plot
summary	Summary parameters from set_summary_parameters
layout	list of additional plotly layout arguments
...	additional arguments

Value

object storing track parameters, for use in plot_tracks

Author(s)

Alicia Schep and Justin Finkle

Examples

library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

## First we'll read in some sample data
genomation_dir <- system.file("extdata", package = "genomationData")
samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
samp.info <- read.table(samp.file, header=TRUE, sep="\t", 
                        stringsAsFactors = FALSE)
samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
ctcf.peaks = genomation::readBroadPeak(system.file("extdata",
                         "wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz",
                          package = "genomationData"))
ctcf.peaks = ctcf.peaks[seqnames(ctcf.peaks) == "chr21"]

## resize peaks to size 1000
ctcf.peaks = resize(ctcf.peaks, width = 10000, fix = "center")

## Make track plotter

track_params <- set_track_parameters(samp.info$fileName[1:3], 
  annotation = TxDb.Hsapiens.UCSC.hg19.knownGene, 
  track_names = samp.info$sampleName[1:3] , 
  share_y = TRUE)
  
if (interactive()){
  plot_tracks(ctcf.peaks[1], track_params)
  plot(ctcf.peaks[1:3], track_params)
}   

skummerf/GenomicWidgets documentation built on May 31, 2019, 6:16 p.m.