PHATE Clustering Error

Question

[fouerghi20]

I am trying to run the PHATE function on the counts matrix I extracted from the Seurat object. After running it and obtaining a PHATE object, I try to run cluster_phate on that object, but I always get this error: Error: object of type 'closure' is not subsettable

This is the code I write which is pretty simple and straightforward:

tumor <-GetAssayData(tumor_mel, slot="counts")

tumor_PHATE <-phate(tumor)

cluster_phate(tumor_PHATE)

The error shows up when I run cluster_phate(). Any help is appreciated!

[fouerghi20]

Still looking for answers/help as the error is still showing up!

[jared.andrews07]

This occurs when you try to use indexing on a function. What actually is tumor_PHATE? Regardless, the github repo for this tool is likely a better place for such questions.

[fouerghi20]

Hi Jared,

tumor_PHATE is the variable that holds the result of running the function phate() on the counts matrix.

[Ram]

Are you sure the phate(tumor) line ran successfully? What is the output of summary(tumor_PHATE)?

[fouerghi20]

Hi RamRS,

Yes, it returns this:

PHATE embedding
knn = 5, decay = 40, t = auto
Data: (18861, 5593)
Embedding: (18861, 2)

[jared.andrews07]

Yes, but what is it? What does running typeof() & class() on it return? Is it a dataframe, a custom class, etc?

[fouerghi20]

the typeof() is "list" and class is "phate" "list"

[fouerghi20]

^ still looking for answers!

[jared.andrews07]

I will again recommend you open an issue in PHATE's github repo. The devs may have some insight as to what's wrong, my guess is that your input is somehow resulting in some weirdness with the PHATE internals that doesn't result in an error, but returns an object that's unexpected.

[fouerghi20]

Thank you so much Jared.