The code is trying to access objects that does not exist in the dataset

[mohan-acog]

Hello,

I'm trying to understand and use Signac. I tried the tutorial with a sample dataset explained here "https://htmlpreview.github.io/?https://github.com/mathewchamberlain/SignacX/master/vignettes/signac-Seurat_pbmcs.html". The initial steps were running fine until the "Signac()" method was called. However, during the runtime, the method is raising the following error
"Error in E@graphs[[1]] : subscript out of bounds". Which seems to be because it was trying to access objects that do not exist in the data. It would be really appreciable if someone could look into this.

Thank you
Mohan

[mathewchamberlain]

Hi Mohan,

Thanks for reaching out. In that tutorial, you can see this sentence:
"Signac actually needs these functions since it uses the nearest neighbor graph generated by Seurat."
It appears that there is no graph object in the Seurat object you are using, e.g., you may have not run these steps:

These are now standard steps in the Seurat workflow for visualization and clustering

pbmc <- RunPCA(pbmc, verbose = FALSE)
pbmc <- RunUMAP(pbmc, dims = 1:30, verbose = FALSE)
pbmc <- FindNeighbors(pbmc, dims = 1:30, verbose = FALSE)

Can you try running these steps, or investigating the naming convention of the graphs in your Seurat object?

Cheers,

Mathew