Question: Plot features on tsne plot with high pLi scores
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gravatar for asmariyaz23
9 days ago by
asmariyaz2310
United States
asmariyaz2310 wrote:

Hello,

I have used Seurat to obtain tsne plot and calculated the DE genes for each cluster. I have pLi scores for each of these DE genes and I want to somehow plot the genes that have pLi score >=0.9 on them. Using FeaturePlot in Seurat I could do 1 gene per plot but I was wondering if there is a better way to represent it on the tsne plot?

Thank you, Asma

seurat rna-seq tsne genes pli • 47 views
ADD COMMENTlink modified 2 days ago by Biostar ♦♦ 20 • written 9 days ago by asmariyaz2310

It can be done in scanpy. Thus it should be similar in seurat. The idea is you give a label to all the genes with pLi score>=0.9, and plot based on the given label.

ADD REPLYlink written 1 day ago by shoujun.gu130
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