Added support for images in SeuratToGiotto function

R/interoperability.R

@@ -1592,8 +1592,15 @@ seuratToGiottoV5 = function(sobject,
       normexp = Seurat::GetAssayData(object = sobject, slot = "counts", assay = 'SCT')
     }
 
-    if(!is.null(slot(sobject, 'assays')[[spatial_assay]]@layers)){
+    if("data" %in% slotNames(sobject@assays[[spatial_assay]])){
+      if(!is.null(slot(sobject, 'assays')[[spatial_assay]]@data)){
+        normexp = Seurat::GetAssayData(object = sobject, slot = "data", assay = spatial_assay)
+     }
+    }
+    if("layers" %in% slotNames(sobject@assays[[spatial_assay]])){
+     if(!is.null(slot(sobject, 'assays')[[spatial_assay]]@layers)){
       normexp = LayerData(object = sobject, assay = spatial_assay)
+     }
     }
 
     # Cell Metadata
@@ -1639,13 +1646,23 @@ seuratToGiottoV5 = function(sobject,
       if (!is.null(Seurat::Images(object = sobject, assay = spatial_assay))) {
         spat_coord = Seurat::GetTissueCoordinates(sobject)
         # spat_coord = cbind(rownames(spat_coord), data.frame(spat_coord, row.names=NULL))
-        colnames(spat_coord) = c("sdimx", "sdimy", "cell_ID")
+
+        if(!("cell" %in% spat_coord)){
+          spat_coord$cell_ID <- rownames(spat_coord)
+          colnames(spat_coord) = c("sdimx", "sdimy", "cell_ID" )
+        }
+        else{
+          colnames(spat_coord) = c("sdimx", "sdimy", "cell_ID")
+        }
+
         spat_loc = spat_coord
-        length_assay <- length(sobject@assays$Vizgen@cells@.Data)
+        length_assay <-length(colnames(sobject))
+        #length_assay <- length(sobject@assays$Vizgen@[email protected])
         spat_datatable <- data.table(cell_ID = character(length_assay),
                                      sdimx = rep(NA_real_, length_assay),
                                      sdimy = rep(NA_real_, length_assay))
-        spat_datatable$cell_ID <- rownames(sobject@assays$Vizgen@cells@.Data)
+        #spat_datatable$cell_ID <- rownames(sobject@assays$Vizgen@[email protected])
+        spat_datatable$cell_ID <- colnames(sobject)
         match_cell_ID <- match(spat_loc$cell_ID, spat_datatable$cell_ID)
         matching_indices <- match_cell_ID
         matching_indices <-  matching_indices[!is.na(matching_indices)]
@@ -1688,6 +1705,46 @@ seuratToGiottoV5 = function(sobject,
 
   #Find SueratImages, extract them, and pass to create seuratobj
 
+  for (i in names(sobject@images)){
+
+    #check if image slot has image in it
+    if("image" %in% slotNames(sobject@images[[i]])){
+    if(!is.null(sobject@images[[i]]@image)){
+
+    # Extract the red (r), green (g), and blue (b) channels
+    r <- as.matrix(sobject@images[[i]]@image[,,1])
+    g <- as.matrix(sobject@images[[i]]@image[,,2])
+    b <- as.matrix(sobject@images[[i]]@image[,,3])
+
+    # Convert channels to rasters
+    r <- raster::raster(r)
+    g <- raster::raster(g)
+    b <- raster::raster(b)
+
+    # Stack the channels and convert to brick
+    rgb_stack <- raster::stack(r, g, b)
+    rgb_raster <- raster::brick(rgb_stack)
+
+    #values rgb_raster
+    values_rgb_raster <- raster::values(rgb_raster)
+
+    # Rescale pixel values to the desired range (0-255) first
+    rescaled_values <- scales::rescale(values_rgb_raster, to = c(0, 255))
+
+    # Then set the rescaled values in the raster object
+    rgb_raster <- raster::setValues(rgb_raster, values = rescaled_values)
+    # Convert to SpatRaster
+    rgb_raster <- as(rgb_raster, "SpatRaster")
+
+    # Create Giotto LargeImage
+    gImg <- createGiottoLargeImage(raster_object = rgb_raster)
+
+    # Plot the image
+    plot(gImg)
+    } 
+   }
+  }
+
 
   gobject = createGiottoObject(exp,
                                spatial_locs = spat_loc,