Exporting lists of genesets within aspects

kharchenkolab / pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

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Exporting lists of genesets within aspects #128

Closed BW093 closed 2 years ago

BW093 commented 2 years ago

Hi,

I was wondering if you could help me out with extracting some data from the pagoda2 UI. I am trying to export the data within each aspect as a table. Is there is a way to download the gene sets, scores and count information that make up these aspects (e.g. in screenshot below i want all the data from the 'genesets in aspect' dataset. .

If this is not yet possible in the UI, but is within R, any help with doing that would also be much appreciated too.

Thank you very much.

evanbiederstedt commented 2 years ago

Hi @BW093

We spoke via email.

Thanks for using pagoda2, and for the detailed issue. Yes, I think this is a reasonable feature request. I hope to have something for you by this weekend.

Best, Evan

evanbiederstedt commented 2 years ago

Hi @BW093

I've added this feature into the pagoda2 frontend app. Basically, users should click on the floppy disk icon/button to export the data shown in the grid as a *csv file. It is a somewhat basic implementation, but I hope it works for your purposes.

This button doesn't retrieve all of the data stored (i.e. there is no sever-side rendering here, it's only client-side); only the data rendered in the grid is downloaded in the *csv.

Here is a screenshot indicating where you should be able to click:

This works now for the grids "Gene sets in Aspect", "Genes in the selected Gene Set", and "Genes in Selected Gene Set".

Best, Evan

yfwang27 commented 2 years ago

Hi @evanbiederstedt ,

Thank you very much for providing a solution to our request. However, when I tried to re-install the new version in R with devtools::install_github('kharchenkolab/pagoda2')

It returns error message as below and it'd be great if you could look into this.

Using github PAT from envvar GITHUB_PAT Error: Failed to install 'pagoda2' from GitHub: HTTP error 401. Bad credentials

Rate limit remaining: 57/60 Rate limit reset at: 2021-12-04 13:54:40 UTC

Thank you very much.

evanbiederstedt commented 2 years ago

Hi @yfwang27

This is a error related to devtools: https://github.com/r-lib/remotes/issues/330

It's not related to pagoda2; please see the discussion in the link above.

In terms of installation, try with CRAN i.e. install.pakcages()