multi-entity proximity and neighborhood analysis

Author: Artur-man

.github/workflows/check.yml

@@ -170,21 +170,13 @@ jobs:
       # All Other dependencies
       - name: Install Suggested dependencies
         run: |
-          # BiocManager::install(c('DelayedArray'))
-          # BiocManager::install(c('DelayedMatrixStats'))
-          # BiocManager::install(c('HDF5Array'))
-          # remotes::install_github('bnprks/BPCells/[email protected]')
-          # devtools::install_github("Huber-group-EMBL/Rarr")
-          # devtools::install_github('BIMSBbioinfo/ImageArray')
-          # devtools::install_github('BIMSBbioinfo/HDF5DataFrame')
-          # devtools::install_github('BIMSBbioinfo/ZarrDataFrame')
           devtools::install_github('BIMSBbioinfo/VoltRonStore')
           install.packages("Seurat")
           BiocManager::install("glmGamPoi")
           install.packages('arrow')
           BiocManager::install('RBioFormats')
           BiocManager::install('ComplexHeatmap')
-          devtools::install_github('dmcable/spacexr')
+          BiocManager::install('spacexr')
           devtools::install_github('xuranw/MuSiC')
           BiocManager::install('SingleCellExperiment')
           BiocManager::install('SpatialExperiment')
@@ -195,7 +187,7 @@ jobs:
           devtools::install_github('vitessce/vitessceR')
           BiocManager::install('TOAST')
           devtools::install_github('xuranw/MuSiC')
-          devtools::install_github('scverse/anndataR')
+          BiocManager::install('anndataR')
           devtools::install_github('drieslab/Giotto')
         shell: Rscript {0}
 

Dockerfile

@@ -39,14 +39,6 @@ RUN R CMD javareconf -e
 USER rstudio
 
 # Install Suggested dependencies
-# 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('Huber-group-EMBL/Rarr')"
-# RUN R -e "options(timeout = 600000000); remotes::install_github('bnprks/BPCells/[email protected]')"
-# RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/ImageArray')"
-# RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/HDF5DataFrame')"
-# RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/ZarrDataFrame')"
 RUN R -e "options(timeout = 600000000); remotes::install_github('BIMSBbioinfo/VoltRonStore')"
 RUN R -e "options(timeout = 600000000); install.packages('Seurat')"
 RUN R -e "BiocManager::install('glmGamPoi')"
@@ -83,7 +75,8 @@ USER root
 
 # Install spacexr
 RUN apt-get install -y libgsl-dev
-RUN R -e "options(timeout = 600000000); devtools::install_github(\"dmcable/spacexr\")"
+# RUN R -e "options(timeout = 600000000); devtools::install_github(\"dmcable/spacexr\")"
+RUN R -e "options(timeout = 600000000); BiocManager::install(\"spacexr\")"
 
 # increase cache disk size for ImageMagick
 RUN sed -i 's/2GiB/10GiB/g' /etc/ImageMagick-6/policy.xml

NAMESPACE

@@ -269,6 +269,7 @@ importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,induced_subgraph)
 importFrom(igraph,make_empty_graph)
 importFrom(igraph,neighborhood)
+importFrom(igraph,set_edge_attr)
 importFrom(igraph,simplify)
 importFrom(igraph,subgraph)
 importFrom(igraph,union)

R/objects.R

@@ -879,10 +879,11 @@ getBlockConnectivity <- function(object, assay) {
         split(names(components$membership), components$membership)
       )
     } else {
-      assay_list <- c(assay_list, cur_assaynames)
+      assay_list <- c(assay_list, split(cur_assaynames, cur_sections))
     }
   }
-
+  names(assay_list) <- NULL
+  
   # return list
   assay_list
 }
@@ -1082,7 +1083,8 @@ subsetVoltRon <- function(
   # subset graphs
   graph_list <- subset_graphs(
     object,
-    spatialpoints = vrSpatialPoints(metadata, assay = vrAssayNames(object))
+    spatialpoints = vrSpatialPoints(metadata, 
+                                    assay = vrAssayNames(object, assay = "all"))
   )
 
   # set VoltRon class