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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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regulons expression plots #23

Closed justinesjw closed 6 years ago

justinesjw commented 6 years ago

Hello,

Thanks for the great work on pySCENIC! been using R version and pySCENIC is so much faster!

Though, I can't seem to find some feature (eg. TSNE, histogram plots) for regulons' expressions that are found in R version of SCENIC. Where can I find them? I may have over looked but may I know where to find the documentation of all the functions available?

Thanks! Justine

bramvds commented 6 years ago

Dear Justine,

Thanks. Unfortunately these features are not yet available in pySCENIC. I'll put them on the todo list (see Projects).

The best alternative is to use the tool SCope (web and standalone versions are available). You export your analysis as a loom file via the export2loom function available in the pyscenic.export module and subsequently view and explore the regulons via SCope.

Another less convenient solution would be to export the data as JSON and use the visualisation features available in R (this feature was requested in the following issue: https://github.com/aertslab/pySCENIC/issues/16).

Hope this helps, Bram

lucygarner commented 4 years ago

Dear Bram,

I am struggling with generating the loom file from the command line output.

The files I have are: merged_all_expr_mat.adjacencies.csv (output from pyscenic grn) regulons.csv (output from pyscenic ctx) auc_mtx.csv (output from pyscenic aucell)

How can I generate the loom file from this using export2loom or another method, so that I can analyse the results using SCope?

Also, where do I find the AUC thresholds in the command line output?

Many thanks, Lucy

yingyonghui commented 4 years ago

Dear Bram,

I am struggling with generating the loom file from the command line output.

The files I have are: merged_all_expr_mat.adjacencies.csv (output from pyscenic grn) regulons.csv (output from pyscenic ctx) auc_mtx.csv (output from pyscenic aucell)

How can I generate the loom file from this using export2loom or another method, so that I can analyse the results using SCope?

Also, where do I find the AUC thresholds in the command line output?

Many thanks, Lucy

@lc822 So have you solved the problem? I just have the same question to find the AUC thresholds from pySCENIC, and any suggestions would be appreciated! Thank you! Ying

lucygarner commented 4 years ago

Hi @yingyonghui,

Unfortunately I haven't found a solution to this yet, as I am having some problems with the earlier stages of the pySCENIC command line workflow.

Best, Lucy

yingyonghui commented 4 years ago

Hi @lc822 , I used pySCENIC in python interface, and I just found the solutions to get the AUC thresholds. Once you get the AUC matrix, try the following codes:

from pyscenic.binarization import binarize auc_mtx_bi = binarize(auc_mtx)

the variable auc_mtx_bi contains the binary matrix and the corresponding thresholds. Best wishes! Ying

lucygarner commented 4 years ago

Perfect, thank you. I will give this a try now that I have the AUC matrix!