Merge pull request #167 from jiajic/dev

Several features and fixes

.github/workflows/covr.yml

@@ -35,7 +35,7 @@ jobs:
           _R_CHECK_RD_XREFS: false
         with:
           dependencies: '"hard"' # do not use suggested dependencies
-          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr,  any::sp, any::stars, any::raster, any::sf
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr,  any::sp, any::stars, any::raster, any::sf,  any::RTriangle, any::geometry
           needs: coverage
 
       - name: Set up dependencies (GiottoData)

.github/workflows/dev_check.yml

@@ -46,7 +46,7 @@ jobs:
           _R_CHECK_RD_XREFS: false
         with:
           dependencies: '"hard"' # do not use suggested dependencies
-          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::knitr, any::rmarkdown, any::sp, any::stars, any::raster, any::sf, any::scattermore, any::exactextractr, github::drieslab/GiottoData
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::knitr, any::rmarkdown, any::sp, any::stars, any::raster, any::sf, any::scattermore, any::exactextractr, any::RTriangle, any::geometry, github::drieslab/GiottoData
 
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2

.github/workflows/main_check.yml

@@ -62,7 +62,7 @@ jobs:
           _R_CHECK_RD_XREFS: false
         with:
           dependencies: '"hard"' # do not use suggested dependencies
-          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::knitr, any::rmarkdown, any::sp, any::stars, any::raster, any::sf, any::scattermore, any::exactextractr, github::drieslab/GiottoData
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::knitr, any::rmarkdown, any::sp, any::stars, any::raster, any::sf, any::scattermore, any::exactextractr, any::RTriangle, any::geometry, github::drieslab/GiottoData
 
       - name: Test python env build
         run: |

DESCRIPTION

@@ -79,10 +79,10 @@ Suggests:
 Remotes: drieslab/GiottoUtils
 Config/testthat/edition: 3
 Collate: 
-    'NN_network.R'
     'package_imports.R'
     'classes.R'
     'generics.R'
+    'NN_network.R'
     'aggregate.R'
     'auxilliary.R'
     'combine_metadata.R'
@@ -137,7 +137,6 @@ Collate:
     'stitch_coordinates.R'
     'subset.R'
     'suite_reexports.R'
-    'visiumImage.R'
     'zzz.R'
 URL: https://drieslab.github.io/GiottoClass/
 VignetteBuilder: knitr

NAMESPACE

@@ -10,7 +10,6 @@ S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
 S3method(t,spatLocsObj)
 S3method(t,spatialNetworkObj)
-export(VisiumV1)
 export(addCellMetadata)
 export(addFeatMetadata)
 export(addGiottoImage)
@@ -77,6 +76,7 @@ export(createGiottoPolygonsFromMask)
 export(createMetafeats)
 export(createNearestNetObj)
 export(createNearestNetwork)
+export(createNetwork)
 export(createSpatEnrObj)
 export(createSpatLocsObj)
 export(createSpatNetObj)
@@ -101,6 +101,7 @@ export(create_spat_locs_obj)
 export(create_spat_net_obj)
 export(cropGiottoLargeImage)
 export(distGiottoImage)
+export(edge_distances)
 export(estimateImageBg)
 export(evaluate_input)
 export(fDataDT)
@@ -289,7 +290,6 @@ export(updateGiottoPointsObject)
 export(updateGiottoPolygonObject)
 export(update_giotto_params)
 export(writeGiottoLargeImage)
-exportClasses(VisiumV1)
 exportClasses(cellMetaObj)
 exportClasses(dimObj)
 exportClasses(exprObj)
@@ -360,12 +360,8 @@ exportMethods(wrap)
 import(GiottoUtils)
 import(data.table)
 import(utils)
-importClassesFrom(SeuratObject,SpatialImage)
 importClassesFrom(terra,SpatExtent)
 importClassesFrom(terra,SpatVector)
-importFrom(GiottoUtils,getDistinctColors)
-importFrom(GiottoUtils,getMonochromeColors)
-importFrom(GiottoUtils,getRainbowColors)
 importFrom(grDevices,dev.size)
 importFrom(graphics,legend)
 importFrom(graphics,par)