integration with Harmony

[prayer-wu]

Hi,

I merge two spatial seurat object.

seurat_obj <- merge(st.list[[1]], st.list[2:length(st.list)])
seurat_obj <- NormalizeData(seurat_obj) %>% FindVariableFeatures() %>% ScaleData()

seurat_obj
An object of class Seurat
26481 features across 170319 samples within 1 assay
Active assay: Spatial (26481 features, 2000 variable features)
3 layers present: counts, data, scale.data
2 images present: P2, P4

seurat_obj$group %>% unique()
[1] "P2" "P4"

then,
seurat_obj <- RunBanksy(seurat_obj,
lambda = 0.5, verbose = TRUE,
assay = "Spatial", slot = "data", features = "variable",
k_geom = 30, group = "group", split.scale = F
)
Fetching data from slot data from assay Spatial
Subsetting by features
Staggering locations by group
Error in [<-.data.frame(*tmp*, , 1, value = c(11602, 11652, 11702, :
replacement has 170319 rows, data has 90708

What should I do?

[jleechung]

Hi @prayer-wu, sorry for the late reply. Can you try re-installing SeuratWrappers from our fork with

remotes::install_github('jleechung/seurat-wrappers')

If that doesn't work, could you try creating a minimal example that reproduces the error? That'll help with debugging.

Thanks!