@gmod/jbrowse
Version:
JBrowse - client-side genome browser
85 lines (57 loc) • 6.46 kB
Markdown
---
id: image_tracks
title: Pre-rendered Image Tracks
---
# Pre-rendered Image Tracks
JBrowse supports tracks based on pre-generated PNG or JPEG images that are tiled along the reference sequence. Currently, JBrowse ships with two different image track generators: [wig-to-json.pl](#wig-to-jsonpl "wikilink"), which generates images showing simple quantitative (wiggle) data, and [draw-basepair-track.pl](#draw-basepair-trackpl "wikilink"), which draws arcs to show the base pairing structure of RNAs.
## wig-to-json.pl
--------------
Using a [wiggle](http://genome.ucsc.edu/goldenPath/help/wiggle.html) file, this script creates a single Image track that displays data from the wiggle file. **Beginning with JBrowse 1.5, this is no longer the recommended method of displaying wiggle data: it has largely been replaced by the direct-access BigWig data store coupled with the next-generation Wiggle track type. See [Wiggle Tracks](/#Wiggle/BigWig_Tracks_(XYPlot,_Density) "wikilink").**
In wiggle data, a numeric value is associated with each nucleotide position in the reference sequence. This is represented in JBrowse as a track that looks like a histogram, where the horizontal axis is for each nucleotide position, and the vertical axis is for the number associated with that position. The vertical axis currently does not have a scale; rather, the heights for each position are relative to each other.
Special dependencies: [libpng](http://www.libpng.org/pub/png/libpng.html)
In order to use wig-to-json.pl, the code for wig2png must be compiled. Normally, this is done automatically by `setup.sh` but it can be done manually if necessary. See the Quick Start Tutorial packaged with JBrowse for details.
### Basic usage
` bin/wig-to-json.pl --wig <wig file> --tracklabel <track name> [options]`
Hint: If you are using this type of track to plot a measure of a prediction's quality, where the range of possible quality scores is from some lowerbound to some upperbound (for instance, between 0 and 1), you can specify these bounds with the max and min options.
|Option|Value|
|------|-----|
|wig|The name of the wig file that will be used. This option must be specified.|
|tracklabel|The internal name that JBrowse will give to this feature track. This option requires a value.|
|key|The external, human-readable label seen on the feature track when it is viewed in JBrowse. The value of key defaults to the value of tracklabel.|
|out|A path to the output directory (default is 'data' in the current directory).|
|tile|The directory where the tiles, or images corresponding to each zoom level of the track, are stored. Defaults to data/tiles.|
|bgcolor|The color of the track background. Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "255,255,255".|
|fgcolor|The color of the track foreground (i.e. the vertical bars of the wiggle track). Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "105,155,111".|
|width|The width in pixels of each tile. The default value is 2000.|
|height|The height in pixels of each tile. Changing this parameter will cause a corresponding change in the top-to-bottom height of the track in JBrowse. The default value is 100.|
|min|The lowerbound to use for the track. By default, this is the lowest value in the wiggle file.|
|max|The upperbound to use for the track. By default, this will be the highest value in the wiggle file.|
### System-specific tips for building wig2png
#### Apple OS X
You need libpng and a C++ compiler; you can get these with [Homebrew](http://mxcl.github.com/homebrew/), [MacPorts](http://www.macports.org/), or [Fink](http://www.finkproject.org/).
Once you have those installed, you need to compile the JBrowse wiggle-processing program. JBrowse includes a makefile to do this, but you may need to add the paths for `libpng` and `png.h` to your compiler's library and include paths. For example, if libpng is in `/usr/X11`, you can run `configure` like this:
` ./configure CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib`
Depending on which OS X you have (and whether you're using MacPorts/fink/etc.), libpng might be somewhere other than `/usr/X11`, like `/opt/local` for example. To find where libpng is, try `locate libpng`.
#### Ubuntu / Debian Linux
Be sure to install the `libpng\#\#` and `libpng\#\#-dev` packages, where `\#\#` is a number such as 12 or 15, depending on the version of Ubuntu.
#### Red Hat/CentOS/Fedora Linux
Be sure to install the `libpng` and `libpng-devel` packages.
# # draw-basepair-track.pl
This script inputs a single base pairing track into JBrowse. A base pairing track is a distinctive track type that represents base pairing between nucleotides as arcs. In addition, it is intended to demonstrate the Perl API for writing your own image track generators.
### Basic usage
`bin/draw-basepair-track.pl --gff <gff file> --tracklabel <track name> [options]`
|Option|Value|
|------|-----|
|gff|The name of the gff file that will be used. This option must be specified.|
|tracklabel|The internal name that JBrowse will give to this feature track. This option requires a value.|
|key|The external, human-readable label seen on the feature track when it is viewed in JBrowse. The value of key defaults to the value of tracklabel.|
|out|A path to the output directory (default is 'data' in the current directory).|
|tile|The directory where the tiles, or images corresponding to each zoom level of the track, are stored. Defaults to data/tiles.|
|bgcolor|The color of the track background. Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "255,255,255".|
|fgcolor|The color of the track foreground (i.e. the base pairing arcs). Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "0,255,0".|
|width|The width in pixels of each tile. The default value is 2000.|
|height|The height in pixels of each tile. Changing this parameter will cause a corresponding change in the top-to-bottom height of the track in JBrowse. The default value is 100.|
|thickness|The thickness of the base pairing arcs in the track. The default value is 2.|
|nolinks|Disables use of file system links to compress duplicate image files.|