TPM instead of FPKM in reference experiments - Issue - ebi-gene-expression-group/atlas-heatmap

Deniaudm commented 7 years ago

Hi!
I included the heatmap as a widget in our website.
The epression level is expressed in FPKM, I'm guessing it's a default setting?
It is also available in TPM on Expression Atlas Website. How can I change the unit on our website? I would like TPM instead of FPKM (or even both). Maybe a parameter in the expressionAtlasHeatmapHighcharts.render function?

Is there a way to have access to all the possible parameters? (a full documentation besides the differents examples)

Thanks for your help!

alfonsomunozpomer commented 7 years ago

Hi @Deniaudm, that is good to hear!

What is your website and how are you including the heatmap? It’d be great to know!

From your issue I guess you’re displaying reference experiments. In the multiexperiment view or in a specific experiment TPMs are returned.

As for all parameters, the supported ones are the ones featured in the showcase gallery, which are pretty much all parameters the render method accepts.

If you’re displaying a reference experiment, as a temporary workaround you can explicitly request the reference experiment accession and the expression units will be TPMs. Would that work until we add a fix?

Deniaudm commented 7 years ago

Thanks for your reply @alfonsomunozpomer!

My website is matrixDB. I included the heatmap as a widget:

expressionAtlasHeatmapHighcharts.render({
target: 'heatmap',
experiment: 'reference',
query: {gene: [" + list + "]}
})

(with "list" a string containing one or several " 'value': 'id' " )

I ran some test using reference experiment accession (E-MTAB-2836) and indeed, the unit is TPM.
It works but it's kinda "disapointing" if we can just display a specific smaller dataset although reference is available just to change the unit.

Or maybe there is an accession corresponding to "reference"?

Thanks again for your help

alfonsomunozpomer commented 7 years ago

Thanks for the feedback, I just saw it in e.g. http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=P51587. I’ve seen that the buttons to the top right are very probably conflicting with your flavour of Bootstrap. I’ll keep it in mind for future fixes, but it looks quite good. :)

You’re right on your second assumption. A reference experiment is one of our data sets hand picked by the curation team that is representative of the species displayed. In this case the data you get by passing experiment: 'E-MTAB-2836' is the same as experiment: 'reference'.

Deniaudm commented 7 years ago

Yes, we get a conflict with Bootsrtap, thanks for a potential future fix :)

We have several species in our database, e.g. http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=P02454

Can you give me (or tell me where I can find) the reference experiment accession of each species, please?

I will be able to automtically display the dataset corresponding to the species of the current page.

Thanks again for your help!

alfonsomunozpomer commented 7 years ago

Here is the authoritative, most up-to-date set of reference experiments:
https://github.com/gxa/atlas/blob/master/base/src/main/java/uk/ac/ebi/atlas/web/ApplicationProperties.java

Also, a bit unrelated, is that we have a mailing list intended for all developers who integrate the package (informally we call it “the widget”) in their services:
https://listserver.ebi.ac.uk/mailman/listinfo/atlas-widget

It’s the best way to keep up with new releases and (sometimes breaking) changes. We try to keep it very low traffic. Have a look, for instance, to all the messages in May, an unusually high activity month for the list standards. :)

Deniaudm commented 7 years ago

That's perfect!
Thanks again for your quick replies, it was very helpful.

I'm gonna suscribe to the mailing list :)