Error when plotting Nanostring CosMx data - No compatible spatial coordinates

[Ikey20]

Hello - I performed unsupervised clustering using Nanostring CosMx data and when I try to plot an ImageDimPlot, it says "No compatible spatial coordinates present". Anyone have any ideas? Thanks!

[huanananan]

use
SpatialDimPlot(spe2, label = TRUE, ) # label.size = 2,pt.size.factor = 3

[shaniAmare]

Make sure you use one of the names in the spatial fields of view present as the fov variable

e.g.

> so
An object of class Seurat 
6519 features across 324581 samples within 3 assays 
Active assay: RNA (6175 features, 500 variable features)
 3 layers present: counts, data, scale.data
 2 other assays present: negprobes, falsecode
 2 dimensional reductions calculated: pca, umap
 2 spatial fields of view present: TMA3 TMA4

x <- "TMA3"
ImageDimPlot(so, fov = x, 
             axes = TRUE, group.by = "celltype", 
             boundaries = "segmentation", cols = cell_cols, 
             border.size = 0.2, border.color = NA, 
             coord.fixed = FALSE) + 
 ggtitle(x)

HTH