spot level conversion for as.SpatialExperiment

Artur-man · Nov 22, 2024 · e085829 · e085829
1 parent 0caf9d1
commit e085829
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Showing 17 changed files with 10,274 additions and 28 deletions.
diff --git a/R/conversion.R b/R/conversion.R
@@ -740,7 +740,7 @@ as.SpatialExperiment <- function(object, assay = NULL, reg = FALSE){
 
   # check Seurat package
   if(!requireNamespace('SpatialExperiment'))
-    stop("Please install SpatialExperiment package!")
+    stop("Please install SpatialExperiment package!: BiocManager::install('SpatialExperiment'')")
 
   # check the number of assays
   if(is.null(assay)){
@@ -754,44 +754,42 @@ as.SpatialExperiment <- function(object, assay = NULL, reg = FALSE){
   }
 
   # check the number of assays
-  if(unique(vrAssayTypes(object, assay = assay)) %in% c("spot","ROI")) {
-    stop("Conversion of Spot or ROI assays into SpatialExperiment is not yet permitted!")
+  if(unique(vrAssayTypes(object, assay = assay)) %in% c("ROI", "molecule", "tile")) {
+    stop("Conversion of ROI, molecule and tile assays into SpatialExperiment is not yet permitted!")
   }
 
   # data
-  rowdata <- vrData(object, assay = assay, norm = FALSE)
+  rawdata <- vrData(object, assay = assay, norm = FALSE)
 
   # metadata
   metadata <- Metadata(object, assay = assay)
+  if(is.null(rownames(metadata)))
+    rownames(metadata) <- metadata$id
   assays <- stringr::str_extract(rownames(metadata), pattern = "_Assay[0-9]+$")
   assays <- gsub("^_", "", assays)
 
   # coordinates
-  coords <- vrCoordinates(object, assay = assay, reg = reg)
+  coords <- vrCoordinates(flipCoordinates(object, assay = assay), assay = assay, reg = reg)
 
   # Seurat object
-  spe <- SpatialExperiment::SpatialExperiment(assay=rowdata,
+  spe <- SpatialExperiment::SpatialExperiment(assay=list(counts = rawdata),
                                               colData=metadata,
                                               sample_id=assays,
                                               spatialCoords=coords)
 
   # get image objects for each assay
   for(assy in vrAssayNames(object)){
     assay_object <- object[[assy]]
-    if(vrAssayTypes(assay_object) == "cell"){
-      img <- vrImages(assay_object)
-      imgfile <- tempfile(fileext='.png')
-      magick::image_write(image = img, path = imgfile, format = 'png')
-      spe <- SpatialExperiment::addImg(spe,
-                                       sample_id = vrAssayNames(assay_object),
-                                       image_id = "main",
-                                       imageSource = imgfile,
-                                       scaleFactor = NA_real_,
-                                       load = TRUE)
-      file.remove(imgfile)
-    } else {
-      stop("Currently VoltRon does only support converting cell type spatial data sets into SpatialExperiment objects!")
-    }
+    img <- vrImages(assay_object)
+    imgfile <- tempfile(fileext='.png')
+    magick::image_write(image = img, path = imgfile, format = 'png')
+    spe <- SpatialExperiment::addImg(spe,
+                                     sample_id = vrAssayNames(assay_object),
+                                     image_id = "main",
+                                     imageSource = imgfile,
+                                     scaleFactor = 1,
+                                     load = TRUE)
+    file.remove(imgfile)
   }
 
   # return

diff --git a/cleanup b/cleanup
@@ -1,4 +1,3 @@
 #!/bin/sh
 rm -f src/Makevars configure.log autobrew
 rm -Rf .deps
-rm -Rf .deps
diff --git a/docs/conversion.html b/docs/conversion.html
@@ -13,7 +13,7 @@
 
 <title>Conversion</title>
 
-<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.29/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />
@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.5.2/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet" />
 
 <style type="text/css">
   code{white-space: pre-wrap;}