Display diploid genotypes on the website

[kimrutherford]

... once we have some in Chado (pombase/pombase-chado#734).

I think this needs a short discussion.

This might be related: #1327

[kimrutherford]

Should the diploids have their own sections on the gene pages? Should we change:

Single locus phenotype
Multi-locus phenotype

to

Single locus haploid phenotype
Multi-locus haploid phenotype
Single locus diploid phenotype
Multi-locus diploid phenotype

(and add to new items to the left hand menu?)

or should we split the "Population phenotype" and "Cell phenotype" sections into sub-sections:

Population phenotype (haploid genotypes)
Population phenotype (diploid genotypes)
Cell phenotype (haploid genotypes)
Cell phenotype (haploid genotypes)

[ValWood]

I thought we envisioned having all of the haploids and then all of the diploids in each table

I wonder if a filter would be better? I can see that it would be nice to see one or the other but:

A It might be useful for users to see them integrated B I suspect for many phenotypes which predated the ability to specify diploids, tant some haploid alleles should really be diploid.

For example anything related to sporulation:

seeing them together might prompt people to tell us where we need to fix.

Then the filter would achieve the same as separate tables (hard to integrate the tables in your head)

[kimrutherford]

Would it be OK to have haploid/diploid filter in the detailed view only? It's easier to implement that way.

[mah11]

re Kim's questions: I think there was a lack of love for splitting the phenotypes into four tables, no matter how they were sliced up ... but that might be another thing I'm remembering from the Canto context (where haploids and diploids have different sections of the same table - see https://github.com/pombase/canto/issues/1941).

re Val's latest comments: I've been finding it hard to spot diploids in the annotation tables; that and the notion of being consistent with Canto prompted my comments. I don't actively like having haploids and diploids interspersed -- there's no advantage for my use cases to "integrating" the annotations that way -- but I could probably make do with a filter.

[kimrutherford]

One simple thing we could do that might help a little is to always put the diploids first when there is a list of genotypes. We could also use a subtly (or not subtly) different style for the diploids. We can change colour or font. Or use bold, underline or italic.

If it helps we can try some changes live on a call so you can see how they look.

[ValWood]

Should we do this on Thursday?

[mah11]

One simple thing we could do that might help a little is to always put the diploids first when there is a list of genotypes.

That won't hurt, although there don't seem to be many terms that have both haploid and diploid genotypes annotated.

If it helps we can try some changes live on a call so you can see how they look.

also can't hurt!

[kimrutherford]

We decided to group the genotypes so that all halpoid genotypes come first, then all diploid genotypes.

We'll add a new filter: #1688

[kimrutherford]

The main site is now splitting genotypes into single/multi locus rather than single/multi alleles.

I've done quite a bit of testing, especially the query builder but please watch out for problems I've missed.

[kimrutherford]

We decided to group the genotypes so that all halpoid genotypes come first, then all diploid genotypes.

I've done that in the summary view. It will take a bit longer to implement in the detailed view. The change will be visible tomorrow morning.

[kimrutherford]

I've done that in the summary view.

I should have said, it's only done for the genotypes at the top of the section which are from annotations without an extension.

[ValWood]

Looks good.

[ValWood]

ready for documentation.

[mah11]

I've just committed updated documentation and a news item (forgot to tag the ticket in the doc'n commits).

[kimrutherford]

I've just committed updated documentation and a news item (forgot to tag the ticket in the doc'n commits).

Thanks! That's all live now.