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msraredon / NICHES

Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
https://msraredon.github.io/NICHES/
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Error: No cell overlap between new meta data and Seurat object #34

Closed suerle closed 2 months ago

suerle commented 6 months ago

Hi,

Thanks for this great tool.

NICHES has worked well for me in the past. However, now I am running into "Error: No cell overlap between new meta data and Seurat object".

I am trying to find ligand receptor networks upregulated in Visium spots with a certain annotation in meta.data column "hotspots".

Here is my code: s12_niche@meta.data$x <- s12_niche@images$caudal_6.5_r_V13Y22.328_D1@coordinates$row s12_niche@meta.data$y <- s12_niche@images$caudal_6.5_r_V13Y22.328_D1@coordinates$col DefaultAssay(s12_niche) <- "Spatial" s12_niche <- SeuratWrappers::RunALRA(s12_niche) s12_niche_output <- RunNICHES(object = s12_niche, LR.database = "fantom5", species = "human", assay = "alra", position.x = 'x', position.y = 'y', k = 4, cell_types = "hotspots", min.cells.per.ident = 0, min.cells.per.gene = NULL, meta.data.to.map = c('orig.ident', 'hotspots'), CellToCell = F,CellToSystem = F,SystemToCell = F, CellToCellSpatial = F,CellToNeighborhood = F,NeighborhoodToCell = T).

Output:

Set cell types as Identity of object internally

Subsetting to populations with greater than 0 cells

3987 distinct cells from 2 celltypes to be analyzed

Limiting ground truth to genes within dataset

Mapping against 2470 ground truth signaling mechanisms Compute edgelist based on mutual nearest neighbors. Error: No cell overlap between new meta data and Seurat object

I would appreciate any help regarding potential issues. Thank you!

jcyang34 commented 2 months ago

this error should be fixed by the most recent version on master branch, feel free to reopen the issue if it still happens