Error in drMat[sc1meta$cellID, ] : subscript out of bounds for 10x HD Spatial Gene Expression

[ATPs]

code

.libPaths(c("/data/p/R/spaceranger-4.0", .libPaths()))

library(Seurat)
library(ShinyCell2)

seu <- qs::qread("/data1/x/partners/xuxi/20250530MSC_EC/20250806space/250806seurat/250828seurat_polygons_rm_lung_keep2_xx250514.qs", nthreads = 40)

scConf <- createConfig(seu)

makeShinyFiles(seu, scConf = scConf, 
               shiny.prefix = "xx250514", shiny.dir = "/data2/pub/web/xcWebServer/db/singlecell/ShinyCell/2025/XuLab_Spatial_Transcriptomics_sample_xx250514")

get error

Error in drMat[sc1meta$cellID, ] : subscript out of bounds

data is processed with seurat, a modified version satijalab/seurat#10028

[ATPs]

satijalab/seurat#9012 (comment)

need to work with the "VisiumV2" class?

library(Seurat)


path_to_visium <- file.path("/path/to/visium")
# this path may need to be adjusted depending on the dataset
path_to_coordinates <- file.path(path_to_visium, "spatial/tissue_positions_list.csv")

image_name <- "visium"
object <- Load10X_Spatial(path_to_visium, slice = image_name)
visium_v2 <- object[[image_name]]

# re-read the tissue coordinates
coordinates <- Read10X_Coordinates(path_to_coordinates, filter.matrix = TRUE)

visium_v1 <- new(
  Class = "VisiumV1",
  assay = visium_v2@assay,
  key = visium_v2@key,
  coordinates = coordinates,
  scale.factors = visium_v2@scale.factors,
  image = visium_v2@image
)

# `Radius` is now calculated on-the-fly, but we can populate the static slot
# in case it's depended on
visium_v1@spot.radius <- Radius(visium_v1)

# align the order of counts and coordinates
visium_v1 <- visium_v1[Cells(object)]

object[[image_name]] <- visium_v1

[ATPs]

https://github.com/ATPs/ShinyCell2

solution in this version