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Add support for VisiumV2 image coordinates in Seurat #20

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Add support for VisiumV2 image coordinates in Seurat #20

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24 changes: 21 additions & 3 deletions R/makeShinyFilesSpatial.R
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Original file line number Diff line number Diff line change
Expand Up @@ -30,16 +30,34 @@ makeShinyFilesSpatial <- function(
sc1image = list()
if(class(obj)[1] == "Seurat"){
if(.hasSlot(obj, "images")){
# coordinates
sc1image$coord <- obj@images[[1]]@coordinates
# coordinates - handle both VisiumV1 and VisiumV2 formats
visium_image <- obj@images[[1]]
if ("VisiumV2" %in% class(visium_image)) {
# New VisiumV2 format - coordinates are in boundaries$centroids
coords <- visium_image@boundaries$centroids@coords
# Convert to expected format with imagecol and imagerow columns
sc1image$coord <- data.frame(
tissue = 1, # Default tissue value
row = NA, # Not available in VisiumV2
col = NA, # Not available in VisiumV2
imagecol = coords[, "x"],
imagerow = coords[, "y"]
)
rownames(sc1image$coord) <- rownames(coords)
} else {
# Traditional VisiumV1 format
sc1image$coord <- visium_image@coordinates
}

# uncropped background image
bg_image <- GetImage(obj, mode = "raster") # background image
# bg_grob <- rasterGrob(bg_image, width=unit(1,"npc"), height=unit(1,"npc"),
# interpolate = FALSE) # background image grob
sc1image$bg_image <- bg_image
# sc1image$bg_grob <- bg_grob

# for cropped image generation in the server.R script
sc1image$lowres <- obj@images[[1]]@scale.factors$lowres
sc1image$lowres <- visium_image@scale.factors$lowres

}
} else {
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