Plot Gene Expression - Githubissues

pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

http://stream.pinellolab.org

GNU Affero General Public License v3.0

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Plot Gene Expression #112

Open babramso opened 3 years ago

babramso commented 3 years ago

Love the tool! Is there some simple code for plotting the expression of a single gene on the subway plots or other plots as a heatmap? I can generate labels for each cluster and plot those but I want to spot check some genes to see exactly which cluster and how much a single gene is expressing in that cluster relative to others. Thanks

huidongchen commented 3 years ago

Hi, thanks for trying STREAM.

I am not sure if i understand it correctly but it sounds to me that what you need here is a heatmap for clustering solution, which seems independent of trajectory analysis. So I guess some general scRNA-seq tools like scanpy might be more suitable to make such a plot.