to_widget: to_widget

In skummerf/GenomicWidgets: interactive visualization of genomics data

Description

Method to convert GenomeTrackWidget to htmlwidgets objects

Usage

## S4 method for signature 'LocusViewList'
to_widget(p)

## S4 method for signature 'LocusSummaryList'
to_widget(p)

## S4 method for signature 'GenomeTrackWidget'
to_widget(p)

## S4 method for signature ''NULL''
to_widget(p)

Arguments

p	GenomeTrackWidget or other object storing plot information

Value

htmlwidgets object

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)
  
example_plot <-  plot_tracks(ctcf.peaks[1], track_params)
class(example_plot)

example_widtet <- to_widget(example_plot)
class(example_plot)   
  
if (interactive()){
  example_plot
  example_widget
}   

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