Error using RunBanksy() in Seurat V5.4.0

[Lord-Kenny]

obj <- RunBanksy(obj,
                 lambda = 0.2, verbose = TRUE,
                 assay = "Spatial", slot= "data", 
                 features = "variable", k_geom = 30)

Fetching data from slot data from assay Spatial
Error:
! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct.
ℹ Please use the layer argument instead.

Session info

packageVersion("Banksy")
[1] ‘1.2.0’
packageVersion("Seurat")
[1] ‘5.4.0’
packageVersion("SeuratObject")
[1] ‘5.3.0’

[jleechung]

Hi @Lord-Kenny, could you provide a minimal reproducible example that throws this error?

Also consider:

1. updating Banksy to the latest version:

remotes::install_github('prabhakarlab/Banksy')

2. installing our fork of SeuratWrappers:

remotes::install_github('jleechung/seurat-wrappers@feat-chunk')

And then try running this:

library(Banksy)
library(Seurat)
library(SeuratData)
library(SeuratWrappers)

InstallData('ssHippo')
ss.hippo <- LoadData("ssHippo")

# Filtering
ss.hippo[['percent.mt']] <- PercentageFeatureSet(ss.hippo, pattern = '^MT-')
ss.hippo <- subset(ss.hippo, percent.mt < 10 &
                     nCount_Spatial > quantile(ss.hippo$nCount_Spatial, 0.05) &
                     nCount_Spatial < quantile(ss.hippo$nCount_Spatial, 0.98))
# Downsample
set.seed(42)
ss.hippo <- ss.hippo[,sample(colnames(ss.hippo), 1e4)]

# Normalize
ss.hippo <- NormalizeData(ss.hippo)
ss.hippo <- FindVariableFeatures(ss.hippo)
ss.hippo <- ScaleData(ss.hippo)

# Run BANKSY
ss.hippo <- RunBanksy(ss.hippo, lambda = 0.2, verbose=TRUE, 
                      assay = 'Spatial', slot = 'data', features = 'variable',
                      k_geom = 15)
ss.hippo


pkgs <- c('Banksy', 'Seurat', 'SeuratData', 'SeuratWrappers', 'SeuratObject')

invisible(sapply(pkgs, function(x) {
  cat(x, ': ', as.character(packageVersion(x)), '\n', sep = '')
}))

This works for me.

Banksy: 1.5.10
Seurat: 5.4.0
SeuratData: 0.2.2.9002
SeuratWrappers: 0.4.0
SeuratObject: 5.3.0