plotColocal() not plotting right object names

[dimitrisokolowskei]

Hi,

First congratulations for such a useful package. I'm following the hoodscanR tutorial and I found this situation where colnames(hoods) from calcMetrics() function return me numbers rather than my seurat object cell type annotation labels. For instance:

spe <- calcMetrics(spe, pm_cols = colnames(hoods))

# Only running colnames
colnames(hoods)
 [1] "1"  "10" "11" "12" "13" "14" "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9" 

Here goes my full code. I'm using Seurat v5.3.1.

seurat <- readRDS("seurat.rds")

# Add XY coordinates into metadata
seurat$coord_x <- seurat@images$fov@boundaries$centroids@coords[,1]
seurat$coord_y <- seurat@images$fov@boundaries$centroids@coords[,2]

# Convert Seurat into SingleCellExperiment format
data <- as.SingleCellExperiment(seurat)

# Run Neighbourhood analysis using hoodscanR
spe <- readHoodData(data, anno_col = "celltypes", pos_col = c("coord_x", "coord_y"))
colData(spe)

plotTissue(spe, color = cell_annotation, size = 1.5, alpha = 0.8)
fnc <- findNearCells(spe, k = 200)
pm <- scanHoods(fnc$distance)
hoods <- mergeByGroup(pm, fnc$cells)
spe <- mergeHoodSpe(spe, hoods)
spe <- calcMetrics(spe, pm_cols = colnames(hoods))
plotColocal(spe, pm_cols = colnames(hoods))

I would appreciate any help on this matter!

[ningbioinfo]

Hi @dimitrisokolowskei , after running readHoodData(), can you show me your table(spe$cell_annotation)?

[dimitrisokolowskei]

Hi @ningbioinfo,

It shows my seurat clusters ID's:

table(spe$cell_annotation)

SSPC      Chondrogenic               SMC            Muscle        Adipocytes      Schwann Cell       Osteoclasts 
30613       21860                    14365            2214           500             220               2235