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monarch-initiative / monarch-legacy

Monarch web application and API
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pheno distributions for genomic features #529

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

instead of an ideogram like #261, i wonder if we can start to approach phenotype distributions in the genome a different way.

what if we were to do something like a 2D array / bubble plot. this would go a long way in an overview page. the cols are chromosomes (or really could be any kind of genomic feature/region), and rows are phenotypes (like broad phenotype categories). the bubbles are scaled by the count of gene-phenotype associations on that region/coordinate.

img_20140911_154540

this seems fairly easy to get you the data, and probably easier to get started with rather than an ideogram. we already can get the gene-phenotype association counts based on a phenotypic category, but we just need to get you the differentiating factor (chromosomes or whatever the cols are). @mellybelly @harryhoch

nlwashington commented 10 years ago

maybe something like this?
http://neuralengr.com/asifr/journals/

harryhoch commented 10 years ago

I like it. We might be able to do something even more than that, but let's start simple...

nlwashington commented 10 years ago

the neat thing might also be with the l.h.s. being drillable, ala the datagraph, so that you can explore down/into the graph while looking at the distribution.

mellybelly commented 10 years ago

@nathandunn this is sort of what we were discussing- need a pheno-chromosomal overview

nlwashington commented 9 years ago

we will have this available via scigraph queries very soon. i can supply a static matrix file for you now. anyone want to take this project on? @davism84 @VincentIII @kshefchek

nlwashington commented 9 years ago

or @seger

jmcmurry commented 8 years ago

THIS! +1 @DoctorBud @harryhoch @yuanzhou let's discuss next week

nathandunn commented 8 years ago

@jmcmurry This is related to #653 . . . assuming the X-axis is a chromosome. I don't think it would be hard to finish up (angularJS + D3) . . . so long as there is upstream phenotype data is linked to the variant information.

http://monarchinitiative.org/labs/chromosome-vis-demo

harryhoch commented 8 years ago

@jmcmurry, yes, absolutely. let's discuss