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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

Work with cellxgene-1.0.0 #64

Closed michaeleekk closed 2 years ago

michaeleekk commented 2 years ago

Didn't test a lot but it seems to be able to build and click some buttons in the UI.

One thing I'm not so sure is the data adaptor changes. It was able to use with in the past but I got an error about __enter__. I guess either there are something changed or I used the wrong data adaptor.

Feel free to edit the PR or let me know so that I could make the PR better.

z5ouyang commented 2 years ago

Thanks for the PR. I will check and make modifications for cellxgene v1. several points I found:

  1. config: The cellxgene requirement file is moved under server folder.
  2. appConfig.is_multi_dataset() was used for "--dataroot" to host several datasets in a folder, instead of one port for a dataset. This enabled CellDepot to host many datasets. Thus it is required, I will try to find a solution for this.