How to plot the correlation?

[levinhein]

Hello. I would like to apply your amazing tool to my current scRNA-seq research projects.

May I ask where I can find the code you used to generate Fig 1B to find the cross-cell scatter correlation from the seurat object?

[zhouzilu]

Hi levinhein, I have uploaded the orignal Python code for creating the above plot.

That being said, I don't think it will address your concern. May I ask what version of Seurat did you use? I can write you a small script to create such plot.

[levinhein]

Hello Dr. Zhou, thank you for your kindness. I'm currently using Seurat version Seurat_4.1.1.

Oh, I use R/Rstudio. Will it also work for that?

Thank you!

[zhouzilu]

Hi levinhein,

I've actually never used Seurat 4+... Will this link be helpful? https://satijalab.org/seurat/articles/essential_commands.html

Personally, I would do it this way:

1. Fetch the gene expression for cTPnet predicted value and your corresponding gene expression (CD8A and CD8B for cTPnet_CD8, see more example of corresponding gene in https://github.com/zhouzilu/cTPnet/blob/master/extdata/Figure1b.py)
2. Use ggplot with geom_point (see example https://ggplot2.tidyverse.org/reference/geom_point.html)

This should give you the plot similar to Figure 1b.