-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
updated readme to indicate using motif density plugin
- Loading branch information
Showing
1 changed file
with
3 additions
and
113 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,117 +1,7 @@ | ||
| # Nucleotide Density Plugin | ||
|
|
||
| [](https://travis-ci.org/bhofmei/jbplugin-nucdens) | ||
| This plugin has been moved to [Motif Density Plugin](https://github.com/bhofmei/jbplugin-motifdens) and will not longer be actively developed. | ||
|
|
||
| Allows the user to create multi-lined heatmaps for different nucleotide contexts. User can set the color for each context, a single color for all contexts, or "random" colors will be chosen (see [below](#color-parameters)). | ||
| Please download and install [MotifDensityPlugin](https://github.com/bhofmei/jbplugin-motifdens) instead. | ||
|
|
||
| ## Special Thanks | ||
| Special thanks to [Colin Diesh](http:https://cmdcolin.github.io/) who inspired components of this plugin. Particularly, the [GC Content plugin](https://github.com/elsiklab/gccontent) (for the storage class) and [Multi BigWig plugin](https://github.com/elsiklab/multibigwig) (for multiple density tracks). | ||
|
|
||
| "Random" color generation was possible thanks to [Chroma.js](https://github.com/gka/chroma.js/). A copy downloaded March 16, 2017 is included in this plugin. | ||
|
|
||
| ## Install | ||
|
|
||
| For JBrowse 1.11.6+ in the _JBrowse/plugins_ folder, type: | ||
| `git clone https://github.com/bhofmei/jbplugin-nucdens.git NucleotideDensityPlugin` | ||
|
|
||
| **or** | ||
|
|
||
| downloaded the latest release version at [releases](https://github.com/bhofmei/jbplugin-nucdens/releases). | ||
| Unzip the downloaded folder, place in _JBrowse/plugins_, and rename the folder _NucleotideDensityPlugin_ | ||
|
|
||
| ## Activate | ||
|
|
||
| Add this to _jbrowse.conf_ under `[GENERAL]`: | ||
| ``` | ||
| [plugins.NucleotideDensityPlugin] | ||
| location = plugins/NucleotideDensityPlugin | ||
| ``` | ||
|
|
||
| If that doesn't work, add this to _jbrowse_conf.json_: | ||
| ```json | ||
| "plugins" : { | ||
| "NucleotideDensityPlugin" : { | ||
| "location" : "plugins/NucleotideDensityPlugin" | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ## Test | ||
| Sample data is included in the plugin to test that the plugin is working properly. With `URL` as the URL path to the JBrowse instance, navigate a web browser to `URL/index.html?data=plugins/NucleotideDensityPlugin/test/data`. | ||
|
|
||
|  | ||
|
|
||
| **Note**: sometimes the density doesn't fully load the first time. Deselect track and readd. | ||
|
|
||
| ## Using Nucleotide Density Tracks | ||
|
|
||
| Loading the track may take awhile for large region and/or many contexts. | ||
|
|
||
| ### Example | ||
| ```json | ||
| { | ||
| "key" : "Nucleotide Density", | ||
| "label" : "nuc_dens", | ||
| "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks", | ||
| "type": "NucleotideDensityPlugin/View/Track/NucleotideDensity", | ||
| "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", | ||
| "context" : ["CG", "CHG", "CHH", "C"] | ||
| } | ||
| ``` | ||
|
|
||
| Sequence contexts must be specified in an array. | ||
| [Degenerate/IUPAC](http:https://www.bioinformatics.org/sms/iupac.html) nucleotides are supported. Gaps are not. Nucleotides can be lowercase or uppercase. | ||
|
|
||
| ### Color Parameters | ||
| For all contexts, density is indicated by the intensity of color. Color is computed as a blend between the background color and specified color weighted by the scaled density. | ||
| Density is scaled to the track configuration `min_score` and `max_score`. | ||
|
|
||
| Color can be specified in four ways. | ||
|
|
||
| 1. Random [default] | ||
| Equidistant colors are assigned to each context based on the number of contexts specified. | ||
| ```json | ||
| "colors": "random" | ||
| ``` | ||
|
|
||
| 2. Single Color | ||
| A single color is used for all contexts. Color can be specified as a string or hexidecimal value | ||
| ```json | ||
| "colors" : "hotpink" | ||
| ``` | ||
|
|
||
| 3. Array | ||
| Colors in the array for assigned to each context based on order. If there are more contexts than colors specified, colors are reused in order. | ||
| ```json | ||
| "colors" : ["red", "orange", "yellow", "greenyellow"] | ||
| ``` | ||
|
|
||
| 4. Object | ||
| Colors can be specified using a javascript object assigning a color to each context. If a context is not assigned a color, the cooresponding "random" color is used. | ||
| ```json | ||
| "colors" : { "CG" : "#A36085", "CHG": "#0072B2", "CHH" : "#CF8F00", "C" : "#00c29b" } | ||
| ``` | ||
|
|
||
| ### Dialog Menu | ||
| Many of the parameters and settings can be adjusted using a dialog box in the track menu. Contexts can be added and removed. Colors can be changed to any of the possible color parameter types. The minimum and maximum density can be set to improve visualization. And the window size and window delta can be adjusted. | ||
|
|
||
|  | ||
|
|
||
|  | ||
|
|
||
| ### Addititional Parameters | ||
| Additional parameters that can be specified for the track configuration. | ||
| * `"min_score" : 0` , minimum density when computing color | ||
| * `"max_score" : 1` , maximum density when computing color | ||
| * `"windowSize" : 100` , window size for sliding window when computing density | ||
| * `"windowDelta" : 10` , window step size for sliding window | ||
| * `"showLabels" : true` , show context sublabels on track | ||
| * `"showScores" : true` , show density value when mouse is over the track | ||
| * `"bothStrands" : false` , use sequence on forward strand only or both strands to compute density | ||
| * `"style" : { "height" : 70 }` , track height | ||
|
|
||
|
|
||
| ## Future Plans | ||
| - "Loading" screen when recomputing after changing a track setting | ||
| - Ability to add track locally by adding option to menu bar, "File" | ||
| - Possibly improved score view (currently works fine but is not visually appealing) | ||
| Source files will be kept in this repository for anyone who may want it. |