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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

Custom selection of VIP features #104

Closed alex-d13 closed 7 months ago

alex-d13 commented 7 months ago

Hi,

I am trying to setup VIP for a large group of users and in order to not overwhelm them and keeping our server resources in check, I wanted to only enable a few selected visualization features in cellxgene VIP, for example violin plots, DGE and heatmaps. I am a bit scared that users will do resource intensive things with the command line feature.

So my question is: is it possible to enable/disable specific features of cellxgene VIP? Would it be enough to create a forked repository and remove a few options from the menu? I was hoping to get your input here :)

Best wishes, Alex

nictru commented 7 months ago

I think the sections can be disabled by commenting out blocks like this

alex-d13 commented 7 months ago

Thats right, I also just tested to comment out the lines in here: https://github.com/interactivereport/cellxgene_VIP/blob/6cdf7f603c6d8f7b1dfa728c9dcaa86a6e547bdd/interface.html#L580

That works as well.

I guess the issue can be closed, except if there is a dedicated way to remove features :)

interactivereport commented 7 months ago

We will add a line in description text file so analyst can disable features.

z5ouyang commented 7 months ago

The functionality ("Disable Panel") is added:

  1. Create a text file the same as the h5ad with file extension ".txt" instead of ".h5ad", in the same folder as h5ad;
  2. The information of this text file will be displayed in the cellxgene left panel between "categorical" and "numerical" variable;
  3. If a line in the text starts with "Disable Panel", side buttons (listed in the text file) in the VIP will NOT be shown, such as: Disable Panel: Command Line Interface, Spatial Transcriptomics
  4. If a line in the text starts with "Initial Embedding", the data will use the specified embedding when user initially access the page , such as: Initial Embedding: harmony_UMAP
  5. If a line in the text starts with "Initial Coloring", the data will use the specified annotation to color the cells when user initially access the page , such as: Initial Coloring: cell_type

Please reopen if you have any additional questions