How to interpret highly variable genes plot in Scanpy?
0
1
Entering edit mode
3.2 years ago
Pratik ★ 1.0k

Hey ya'll,

How do I interpret this plot in the Scanpy Tutorial https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html:

sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5)

extracting highly variable genes
    finished (0:00:00)
--> added
    'highly_variable', boolean vector (adata.var)
    'means', float vector (adata.var)
    'dispersions', float vector (adata.var)
    'dispersions_norm', float vector (adata.var)

enter image description here I understand that the algorithm is identifying highly variable genes, but I don't quite understand what the y-axis means by

dispersions of genes

Any help would be appreciated!

python single-cell RNA Seq • 1.8k views
ADD COMMENT
0
Entering edit mode

Hello! I am going through scanpy and have the same doubt. Have you reached a conclusion on how to interpret the data presented by these graphs?

ADD REPLY

Login before adding your answer.

Traffic: 2065 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6