No image from Seurat object

[GCAT01]

I was running into the same error as #309 however my cellchat object does not contain an image.

> cellChat@images
list()

I created this cellchat object from a Seurat object with an image included

> s_obj@images
$slice1
Spatial coordinates for 2784 cells
Default segmentation boundary: centroids 
Associated assay: Spatial 
Key: slice1_ 

I created the object using the following

cellChat <- createCellChat(s_obj, group.by = "sctype_classification",
                           assay = "SCT", coordinates = spatial.locs,
                           spatial.factors = spatial.factors)

Any thoughts?

[alipirani88]

Thanks for mentioning the issue. I am still waiting for this issue to be resolved. Let me know if you find a solution.

[sqjin]

@GCAT01 @alipirani88 Due to the different spatial technologies, one of the better way is to manually create spatial.factors, see https://github.com/jinworks/CellChat/issues/309 and our tutorial of CellChat_analysis_of_multiple_spatial_transcriptomics_datasets