Running PHATE on Seurat Object

Question

[fouerghi20]

I have single cell data from one sample that I am trying to run through the Seurat pipeline. After having obtained the UMAP plot, I am trying to compare it to the PHATE plot. However, I can't seem to run PHATE on a Seurat object. What are some ways I can go about this? Can I convert my Seurat object to some other data type and run the function on it? is there a PHATE function in Seurat?

Answer 1

[jared.andrews07]

PHATE runs on count matrices. Just extract your counts from the Seurat object via GetAssayData() and go from there.

[fouerghi20]

Hi Jared,

Thank you for the response. I am wondering what the difference is between the count and data options that could be generated by GetAssayData(). Thank you for your help.

[jared.andrews07]

I highly suggest you read their introductory vignette and read the documentation for key analysis steps.

In short, counts are just raw counts that you fed in for each sample (assuming you've done no integration or anything). "data" contains the normalized counts after performing NormalizeData() or SCTransform().