updated for v0.5

README.md

@@ -2,11 +2,9 @@
 
 This is a JBrowse plugin
 
-Allows the user to create multi-lined heatmaps for differente nucleotide contexts. Usr can set the color for each context. Initial intended use is for CG, CHG, and CHH frequency.
-
+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]).
 ##Special Thanks
-Special thanks to [Colin] who inspired components of this plugin. Particularly, the GC Content plugin (for the stor class) and Multi BigWig plugin (for multiple density tracks).
-Additionaly, special thanks for Erik Lyons for the color dialog.
+Special thanks to [Colin Diesh](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).
 
 ##Install
 
@@ -29,6 +27,68 @@ Add this to _jbrowse.conf_ under `[GENERAL]`:
 If that doesn't work, add this to _jbrowse_conf.json_:
 ```
  "plugins" : {
- "NucleotideDensityPlugin" : { "location" : "plugins/NucleotideDensityPlugin" }
-}
-```
+ "NucleotideDensityPlugin" : { 
+ "location" : "plugins/NucleotideDensityPlugin"
+ }
+ }
+```
+
+##Using Nucleotide Density Traacks
+###Example
+ { 
+ "key" : "Nucleotide Density",
+ "label" : "nuc_dens",
+ "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
+ "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+ "context" : ["CG", "CHG", "CHH", "NNN"]
+ }
+
+Sequence contexts must be specified in an array. 
+[Degenerate/IUPAC](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. 
+```
+ "colors": "random"
+```
+
+2. Single Color 
+A single color is used for all contexts. Color can be specified as a string or hexidecimal value
+```
+ "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.
+```
+ "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.
+```
+ "colors" : { "CG" : "#A36085", "CHG": "#0072B2", "CHH" : "#CF8F00", "CH" : "#88C043" }
+```
+
+![Example for color parameters]('img/example_colors.png')
+
+###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
+* `"bothStrands" : false` , use sequence on forward strand only or both strands to compute density
+* `"style" : { "height" : 70 }` , track height
+
+
+##Future Plans
+- Show pixel score along track for each sequence context
+- Ability to add track locally by adding option to menu bar, "File"

release_notes.txt

@@ -1,5 +1,10 @@
 # Release notes
 
+v0.5 - Nov 11, 2016
+- functional dialog box to add/remove contexts, set colors, change window size/delta, and min/max density
+- check box in track menu to use both strands or forward only to compute density
+- removed non-functional "Change score range" option in track menu
+
 v0.2 - Nov 10, 2016
 - allows specifiying unlimited number of nucleotide contexts
 - multiple options to specify color of contexts default to random (not truly random but equidistant colors)