pombase / website

PomBase website v2
MIT License
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Quick little tool to analyse gene lists #842

Closed ValWood closed 6 years ago

ValWood commented 6 years ago

Kim wished that figure 3 was interactive. fig3_conserved_unknown_breakdown

This lead to a little discussion. We decided it would be nice to try to create a quick little gene list viewer that does this.

Basically user supplies a list, and then choose from a set of pre-configured sorting options (later potential to extend)

Quick Mockup:

kim_mock_up

Will try it with a few simple of "classifiers"

That's enough for now, will add more after prototype ;)

kimrutherford commented 6 years ago

I've had a look at how this could be implemented and I think I have a plan. A prototype with one or two data types from your list would take two-ish days I think. Getting something ready to release might take a week but I'm not sure. I'll chip away at this in the background over the next couple of weeks and I'll let you know when there's a prototype.

Git branch: https://github.com/pombase/website/tree/gene-results-vis-experiment

ValWood commented 6 years ago

that would be brilliant, well worth the time investment!

kimrutherford commented 6 years ago

I know I was the one to suggest making the tool vertical but I now think horizontal might work better because most screens are wider than they are tall.

ValWood commented 6 years ago

I don't know. For long lists the image will be longer or wider than a screen It's easier to scroll up down than left/right

kimrutherford commented 6 years ago

Here's my progress so far:

vis-tool-1

ValWood commented 6 years ago

So exciting! Feature size is a good one. This classifier will help me to "analyse" the species specific unknowns! I ditched this for the paper as I couldn't face doing another "figure 3"

kimrutherford commented 6 years ago

Feature size is a good one.

In case it's not clear, "feature size" is the height of the genes lines.

ValWood commented 6 years ago

OK got you, that will be useful too!

kimrutherford commented 6 years ago

I've added a button on the gene lists to go into "Visualise" mode. The button is only shown on pombase-dev for now because the visualisation doesn't do much and looks naff. I'll let you as it improves.

vis-tool-2

http://pombase-dev.bioinformatics.nz/term_genes/GO:0000070

ValWood commented 6 years ago

Oh fab...its useful already.

I just used on (GO:0140223), and I thought there was something wrong since the essentials was so high, but it really is 44/50 (not surprising now I think about it)

It will be so cool! try with "all inviable" from common queries, the try to see what the green ones are

ValWood commented 6 years ago
kimrutherford commented 6 years ago

I've added a GO component option and fixed a bunch of bugs (although there are more to fix). If you click each sort button you get a nice pattern. This screenshot is from http://pombase-dev.bioinformatics.nz/term_genes/GO:0046872

vis-tool-4

ValWood commented 6 years ago

Cool, it seems like you got the basics!

kimrutherford commented 6 years ago

presence/absence from S. cerevisiae (2 classes)

I've added this column. I hope it's what you meant. I also added a column for presence/absence of a human ortholog because it was easy.

I've fixed some display bugs too.

vis-tool-5

ValWood commented 6 years ago

Oh my god this is so cool!

It's great for a quick data check. For example with DNA replication, you can see immediately that all are nuclear except 2 which are mitochondrial.

We can do slightly cleverer within column sorting but it is working really well already!

ValWood commented 6 years ago

Actually the sorting might be OK, you can 'keep shuffling' to get what you want.

A tiny tweak, in the "human present" can you put present to the top rather than absent?

ValWood commented 6 years ago
ValWood commented 6 years ago

Great for spotting "outliers" tRNA metabolism. til1, top bar (no cerevisiae, no human, inviable mitochondrial ....just doesn't happen) That should definitely be on the student list for ortholog detection.

outliers

kimrutherford commented 6 years ago

A tiny tweak, in the "human present" can you put present to the top rather than absent?

I've done that. I've also changed it to sort "viable" ahead of "inviable" as that seemed more consistent.

add product line next to gene ID

Done.

ValWood commented 6 years ago

Let me know if/when you want suggestions/list of what to include.

Like

I didn't mean to start the list now ;) ...I think this will be very, very useful for some people.

ValWood commented 6 years ago

I've done that. I've also changed it to sort "viable" ahead of "inviable" as that seemed more consistent.

kimrutherford commented 6 years ago

Allow blocks to be selected as subsets, to enable drill down

I've done that now. You can click on a block or a gene to toggle the selection. control-click to add the hightlight genes to the selection rather than toggling. I'm still working on the formatting of the list.

vis-tool-select-1

Antonialock commented 6 years ago

This looks great Kim!

It would be nice if the text + gene list moved when you look up and down the list.

The text only displays at the top and disappears when you are not mousing over a block

Here I can see the text because I am mousing over a block at the top of the page:

screen shot 2018-08-05 at 22 23 42

so here I have scrolled down the page and I am mousing over a block, but i can't see the text because it is displayed at the top

screen shot 2018-08-05 at 22 23 51
ValWood commented 6 years ago

this is equivalent to the item above

ValWood commented 6 years ago

You can click on a block or a gene to toggle the selection.

nice. Maybe the list does not need to be presented on the page, but you need to load it if you want to see it?

kimrutherford commented 6 years ago

Maybe the list does not need to be presented on the page, but you need to load it if you want to see it?

I added it for debugging and for now it's the only way to navigate to a gene page - the genes in the selected list are links.

ValWood commented 6 years ago

I'm closing this it's too long. I'll make a new ticket with outstanding tasks classified as pre-release and post-release.