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Elbow plot question (scRNA seq data analysis - scanpy tutorial)

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I am following the tutorial https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering-2017.html for learning purposes.

In the Scree/Elbow plot made in the tutorial - (https://i.sstatic.net/lQxpQyA9.png)

What is represented on the x and y axis why are the values given on y-axis negative Clear understanding of elbow plot.

Thanks

scanpy
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written by ojaswinipandey • ojaswinipandey

1 answer

The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between 0.0 and 1.0) has been log-transformed.

The x axis has each principal component in order from PC 1 to whatever the cutoff is (PC 31 in this case).

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written by Dave Carlson Dave Carlson

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