elsiklab/gwasviewer

A JBrowse plugin for viewing GWAS data

gwasviewer's Issues

Allow autoscaling to scores

scoreFun and style color

@elsiklab,

I am new to javascript, would you please show me how to write scoreFun and the style based on the p-value score. I loaded the plot and the Y axis doesn't show the entire data, I changed to maxHeight to 250 still missing some data point. The data looks like this:

chr1	9940342	9940342	NMNAT1	2.81e-10
chr1	9941343	9941343	LZIC	4.5e-05
chr1	1064776	1064776	C1orf159	6.78e-06
chr1	9941922	9941922	NMNAT1	2.56e-10
chr1	9941922	9941922	LZIC	1.21e-05
chr1	9941923	9941923	RBP7	2.59e-06

Best,
@demis001

Missing License

Howdy @cmdcolin just going through all the plugins listed in the jbrowse plugin repo, and this was missing an explicit license.

Same for https://github.com/elsiklab/myvariantviewer https://github.com/elsiklab/ga4ghviewer https://github.com/elsiklab/qualityglyphs https://github.com/elsiklab/multivariantviewer https://github.com/elsiklab/agp_parser

Add LD tag coloring example

onClick event and legend

Is it possible to show onClick event with this plugin? How you add the color legend to the figure you showed, the config does not exist in the example you provided in github?

view methylation data

I have a bed file similar to this one, the last column is a methylation ratio. I added the *.bed.gz file to the webroot and added the following conf. But, it didn't work, I have installed the other plugin including this one. Any idea?

{
"maxFeatureScreenDensity": 6,
"storeClass" : "JBrowse/Store/SeqFeature/BEDTabix",
"urlTemplate" : "../../rawData/data.bed.gz",
"label" : "brain_GCmap_vPlotter",
"type" : "GWASViewer/View/Track/VariantPlotter"
}

chr1 147971108 147971158 id-1 0.590000
chr1 147971146 147971196 id-2 0.120000
chr1 147971184 147971234 id-3 0.110000
chr1 147971222 147971272 id-4 0.760000

BEDTabix class missing

I can't load the plugin.The default Jbrowse does'nt have
"storeClass" : "JBrowse/Store/SeqFeature/BEDTabix"

Where can I get this? Thx

Y-axis bar shows up smaller than track height before data is loaded

Should make y-axis bar equal to the track height at startup