Error in as(object@graphs$RNA_snn, "dgCMatrix") about swne HOT 4 CLOSED

Hi, can you check if your Seurat object was generated with Seurat V3?

Also, make sure that the SNN was actually built with FindNeighbors. Something like:

obj <- FindNeighbors(obj, dims = 1:20)

Let me know if that works!

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Hi, Thank you for you replay.
Yes I am using Seurat V3.
The issue occurred while I used a V3 object generated by integrating 4 samples (after FindIntegrationAnchors, IntegrateData, RunUMAP, FindNeighbors and FindClusters).
If I use a V3 object generated by analyzing one sample, the swne run smoothly and showed good picture.
Is there any way to apply swne on a Seurat object with integrated samples?
Thank you very much.

from swne.

Ah so RunSWNE doesn't work on integrated Seurat objects yet, hopefully I'll have that functionality up soon.

For now, try using this walkthrough: https://yanwu2014.github.io/swne/Examples/multiple_pancreas_alignment_swne.html

from swne.

Hi, it works well with the workflow you provided. Thank you very much for your help.

from swne.