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

Question

[ojaswinipandey]

0

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

Answer 1

[Dave Carlson]

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).

[ojaswinipandey]

Thank you so much Dave.