"View pathway coverage" visualisation action from gene list?

[kimrutherford]

Would it useful to have a new action on the gene list pages that worked a bit like the slim actions but showed which pathways contain genes from the list, along with the count of the number of genes?

I'm thinking that the count could be a link to a gene results page with the genes from the original list that are in the pathway. And a separate link to the pathway diagram with the genes highlighted.

A mock up for the essential gene case (I made up the numbers):

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[ValWood]

definitely!

[kimrutherford]

Here's my prototype using the essential gene list:
https://desktop.kmr.nz/subset-count:gomodel/from/id/b1e0a0f6-8a25-4fef-8cdd-6e8ca9a93b8a

[ValWood]

git7 in the first list is coloured, but none in the other lists (but you probably know that)

[kimrutherford]

git7 in the first list is coloured, but none in the other lists (but you probably know that)

Do you mean it's coloured here?: https://desktop.kmr.nz/gocam/docs/66187e4700003150

I think that's because gocam-viz gives a different background colour to activities that are directly annotated as "molecular_function".

[kimrutherford]

I think that's because gocam-viz gives a different background colour to activities that are directly annotated as "molecular_function".

I've followed the same colour scheme in my dodgy viewer:
https://www.pombase.org/gocam_view/full/66187e4700003150

[kimrutherford]

I've released the changes on the dev site: https://dev.pombase.org/query
It should be faster than my desktop because dev runs on oliver1.

[ValWood]

I think that's because gocam-viz gives a different background colour to activities that are directly annotated as "molecular_function".

ah OK!

[ValWood]

I've released the changes on the dev site: https://dev.pombase.org/query
It should be faster than my desktop because dev runs on oliver1.

Very nice!

[kimrutherford]

Now with a "Highlight in pathway" link to my dodgy pathway viewer:
https://dev.pombase.org/subset-count:gomodel/from/id/3e36850b-deb0-45fb-ae86-0333b7881735

(dev site only)

We'll be able to link to the gocam-viz widget once this is implemented:

• Highlight specific gene(s) geneontology/wc-gocam-viz#75

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[kimrutherford]

Maybe we need to highlight activities enabled by complexes that contain any of the genes from the gene list?