Merge pull request #243 from BIMSBbioinfo/dev

updates for 0.2.2

Author: Artur-man

.github/workflows/check.yml

@@ -152,7 +152,7 @@ jobs:
           BiocManager::install(c('DelayedMatrixStats'))
           BiocManager::install(c('HDF5Array'))
           remotes::install_github('bnprks/BPCells/r@v0.3.0')
-          devtools::install_github("Artur-man/Rarr@voltron")
+          devtools::install_github("Huber-group-EMBL/Rarr")
           devtools::install_github('BIMSBbioinfo/ImageArray')
           devtools::install_github('BIMSBbioinfo/HDF5DataFrame')
           devtools::install_github('BIMSBbioinfo/ZarrDataFrame')

DESCRIPTION

@@ -30,7 +30,7 @@ License: MIT + file LICENSE
 SystemRequirements: OpenCV 4.8 (or higher): libopencv-dev (Debian, Ubuntu) or 
                     opencv-devel (Fedora)
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 biocViews:
 Imports: methods, grDevices, data.table, Matrix, S4Arrays, S4Vectors, 
          ids, RcppAnnoy, RANN, igraph, dplyr, ggplot2, ggrepel, ggpubr, 

Dockerfile

@@ -33,7 +33,7 @@ RUN R -e "BiocManager::install(c('EBImage', 'S4Arrays', 'BiocSingular'))"
 RUN R -e "BiocManager::install(c('DelayedArray'))"
 RUN R -e "BiocManager::install(c('DelayedMatrixStats'))"
 RUN R -e "BiocManager::install(c('HDF5Array'))"
-RUN R -e "devtools::install_github('Artur-man/Rarr@voltron')"
+RUN R -e "devtools::install_github('Huber-group-EMBL/Rarr')"
 RUN R -e "options(timeout = 600000000); remotes::install_github('bnprks/BPCells/r@v0.3.0')"
 RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/ImageArray')"
 RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/HDF5DataFrame')"

NAMESPACE

@@ -54,6 +54,7 @@ export(getDiffExp)
 export(getFeatures)
 export(getHotSpotAnalysis)
 export(getNicheAssay)
+export(getOmeTiffChannels)
 export(getPCA)
 export(getProfileNeighbors)
 export(getRcppAutomatedRegistration)
@@ -70,6 +71,7 @@ export(importGeoMx)
 export(importImageData)
 export(importOpenST)
 export(importPhenoCycler)
+export(importQuPathIF)
 export(importSTOmics)
 export(importVisium)
 export(importVisiumHD)

NEWS.md

@@ -2,3 +2,8 @@
 
 * Added 'channels' arguement to `ImportImageData` to parse only requested channels 
   from OME-TIFF files.
+  
+* Multi-omic clustering with multiple feature sets and tutorials 
+
+* Added `importQuPathIF` function to generate QuPath processed spatial
+proteomics data as a VoltRon objects

R/allclasses.R

@@ -24,8 +24,9 @@ suppressMessages({
       members = c(
         "matrix",
         "data.frame",
-        "dgRMatrix",
-        "dgeMatrix",
+        # "dgRMatrix",
+        # "dgeMatrix",
+        "Matrix",
         "Array",
         "IterableMatrix"
       )
@@ -127,9 +128,10 @@ suppressWarnings({
     "data_matrix",
     members = c(
       "matrix",
-      "dgCMatrix",
-      "dgRMatrix",
-      "dgeMatrix",
+      # "dgCMatrix",
+      # "dgRMatrix",
+      # "dgeMatrix",
+      "Matrix",
       "Array",
       "IterableMatrix"
     )

R/clustering.R

@@ -195,9 +195,9 @@ getClusters <- function(
   embedding_names <- vrEmbeddingNames(object)
   if (data.type %in% embedding_names) {
     # get data
-    vrdata <- vrEmbeddings(object, assay = assay, type = data.type, dims = dims)
+    vrdata <- vrEmbeddings(object, assay = assay_names, type = data.type, dims = dims)
   } else if (!is.null(data.type)) {
-    vrdata <- t(vrData(object_subset, norm = data.type == "norm"))
+    vrdata <- t(vrData(object_subset, assay = assay_names, norm = data.type == "norm"))
   }
 
   # clustering

R/conversion.R

@@ -508,11 +508,11 @@ as.AnnData <- function(
         }
       }
       X <- make_numpy_friendly(t(data))
-      obsm <- list(
-        spatial = coords,
-        spatial_AssayID = coords,
-        segmentation = segmentations_array
-      )
+      # obsm <- list(
+      #   spatial = coords,
+      #   spatial_AssayID = coords,
+      #   segmentation = segmentations_array
+      # )
       adata <- anndata$AnnData(X = X, obs = metadata, obsm = obsm, uns = uns)
       adata <- reticulate::r_to_py(adata)
       adata$write_zarr(file)
@@ -534,11 +534,11 @@ as.AnnData <- function(
             }
           }
           X <- make_numpy_friendly(t(data))
-          obsm <- list(
-            spatial = coords,
-            spatial_AssayID = coords,
-            segmentation = segmentations_array
-          )
+          # obsm <- list(
+          #   spatial = coords,
+          #   spatial_AssayID = coords,
+          #   segmentation = segmentations_array
+          # )
           adata <- anndata$AnnData(
             X = X,
             obs = metadata,
@@ -593,11 +593,12 @@ as.AnnData <- function(
         var_names = rownames(data),
         X = t(data),
         obs = metadata,
-        obsm = list(
-          spatial = coords,
-          spatial_AssayID = coords,
-          segmentation = segmentations_array
-        ),
+        obsm = osbm,
+        # obsm = list(
+        #   spatial = coords,
+        #   spatial_AssayID = coords,
+        #   segmentation = segmentations_array
+        # ),
         uns = uns
       )
 
@@ -621,11 +622,12 @@ as.AnnData <- function(
       adata <- anndata::AnnData(
         X = t(data),
         obs = metadata,
-        obsm = list(
-          spatial = coords,
-          spatial_AssayID = coords,
-          segmentation = segmentations_array
-        ),
+        obsm = obsm,
+        # obsm = list(
+        #   spatial = coords,
+        #   spatial_AssayID = coords,
+        #   segmentation = segmentations_array
+        # ),
         uns = uns
       )
 

R/image.R

@@ -1606,7 +1606,7 @@ demuxVoltRon <- function(
     if (max(imageinfo$height, imageinfo$width) > max.pixel.size) {
       # scale keypoints
       if (inherits(images, "ImgArray")) {
-        n.series <- length(images@series)
+        n.series <- length(images@levels)
         cur_width <- imageinfo$width
         cur_height <- imageinfo$height
         for (ii in 2:n.series) {