Would be really cool to add intron/exon structure to the graph.
But amazing - definitely in the right direction - the visualisation help give an idea of the overall picture of the gene and will help with identifying parts of the gene that are more interesting to look at…
Gene structure as @Ismail M already mentioned, but I will have to add that as an endpoint, we already have the data in the new tables. One for me
The connection between table and plot is a bit confusing to me having two lanes at different heights. I would rather highlight the variant hovered over in the table if any, and shade the rest. Also, it would be amazing to have a clickable plot, you click on a variant and the table is positioned in that variant.
The Y-axis. The variants overlap a lot as they tend to group in exons, that makes it difficult to understand how many variants we have a in a given region, to circumvent this problem I suggest two approaches: 1) add the -log(AF) to the Y-axis and 2) add an additional line plot below which shows the density distribution
The size of the variant. I would rather use our internal frequency, ie: how many individuals have this variant within phenopolis. Is this something we can provide as a global metric despite user authorization?
Color. First, we need a legend. Second, you could use a simplification of categories like the one described here in SnpEff https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details. Hardcode the map from your effects to impact for which there are just 4 categories: LOW, MODERATE, MODIFIER and HIGH
The variant tooltip. I would build something nicer like 22:12345 A>G instead of the current 22-12345-A-G . Given that the AF represents something in the plot, add whatever AF is used to the tooltip. In the same way that the x-axis add commas to the positions it would be nice to have that in the tooltip too, it is more consistent with the whole thing and easier to read (ie: 1,234,567 instead of 1234567). (I would add those commas to the table too).
The title of the plot, I believe has the chromosome twice TTL5:14:chr14:...
You can probably add a limit to the zoom in, maybe 10 bp? right you zoom in infinitely.
The name of this plot in the selector above is Genome I would rather name it Gene viewer or something with the word gene in it
Migrated from https://github.com/phenopolis/phenopolis_frontend_react/issues/263 Originally created by @pontikos on Thu, 29 Oct 2020 10:02:53 GMT
Would be really cool to add intron/exon structure to the graph.
But amazing - definitely in the right direction - the visualisation help give an idea of the overall picture of the gene and will help with identifying parts of the gene that are more interesting to look at…