h5ad for HashSolo & solo .pdf plots output

[DanSchnell]

Hi,

I'd like to run HashSolo on an experiment, but am not sure about the structure/specification of the h5ad input file...

Is there anything beyond reading it into an anndata object & writing out the h5?

Also, ran solo on the (a?) pbmc dataset but the 4 .pdf files did not appear in the solo_out directory... Should they automatically be produced?

Thanks much!

[njbernstein]

Hi there,

Nope. Nothing else extra. Although make sure your cells are your rows so youll need to transpose your table above.

For more info about anndata see here: http://falexwolf.de/blog/171223_AnnData_indexing_views_HDF5-backing/

I'll investigate the plotting issue

[DanSchnell]

Thanks very much for this guidance & looking into the plotting. From: njbernstein ***@***.***> Reply-To: calico/solo ***@***.***> Date: Wednesday, May 12, 2021 at 12:34 PM To: calico/solo ***@***.***> Cc: "Schnell, Daniel (Dan)" ***@***.***>, Author ***@***.***> Subject: Re: [calico/solo] h5ad for HashSolo & solo .pdf plots output (#63) ***This email originated from an EXTERNAL sender to CCHMC. Proceed with caution when replying, opening attachments, or clicking links in this message.*** Hi there, Nope. Nothing else extra. Although make sure your cells are your rows so youll need to transpose your table above. For more info about anndata see here: http://falexwolf.de/blog/171223_AnnData_indexing_views_HDF5-backing/ I'll investigate the plotting issue — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#63 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJIX34MW4GUXEK67SWHUJWLTNKUW7ANCNFSM44STPSHQ>.