@@ -66,6 +66,9 @@ lisaClust <-

            lisaFunc = "K",

            minLambda = 0.05) {

     if (methods::is(cells, "SummarizedExperiment")) {

+      

+      cells <- cells[,order(cells[[imageID]])]

+      

       cd <- spicyR:::.format_data(

         cells, imageID, cellType, spatialCoords, FALSE

       )

@@ -85,33 +88,36 @@ lisaClust <-

       SummarizedExperiment::colData(cells)[regionName] <- regions

     } else if (is(cells, "data.frame")) {

+      

+      cells <- cells[order(cells[[imageID]]),]

+      

       cd <- cells

       cd <- cd[, c(cellType, imageID, spatialCoords)]

       colnames(cd) <- c("cellType", "imageID", "x", "y")

       cd$cellID <- as.character(seq_len(nrow(cd)))

-            cd$imageCellID <- as.character(seq_len(nrow(cd)))

-

-            lisaCurves <- lisa(cd,

-                Rs = Rs,

-                BPPARAM = BPPARAM,

-                window = window,

-                window.length = window.length,

-                whichParallel = whichParallel,

-                sigma = sigma,

-                lisaFunc = lisaFunc,

-                minLambda = minLambda

-            )

-

-            kM <- kmeans(lisaCurves, k)

-            regions <- paste("region", kM$cluster, sep = "_")

-

-            cells[regionName] <- regions

-        } else {

-            stop(

-                "Unsupported datatype for cells: please use",

-                "SingleCellExperiment or SpatialExperiment"

-            )

-        }

-

-        cells

+      cd$imageCellID <- as.character(seq_len(nrow(cd)))

+      

+      lisaCurves <- lisa(cd,

+                         Rs = Rs,

+                         BPPARAM = BPPARAM,

+                         window = window,

+                         window.length = window.length,

+                         whichParallel = whichParallel,

+                         sigma = sigma,

+                         lisaFunc = lisaFunc,

+                         minLambda = minLambda

+      )

+      

+      kM <- kmeans(lisaCurves, k)

+      regions <- paste("region", kM$cluster, sep = "_")

+      

+      cells[regionName] <- regions

+    } else {

+      stop(

+        "Unsupported datatype for cells: please use",

+        "SingleCellExperiment or SpatialExperiment"

+      )

     }

+    

+    cells

+  }