Merge branch 'dev' into dev

drieslab · Aug 30, 2024 · 93bfde8 · 93bfde8
2 parents e8858a3 + 1e5d90e
commit 93bfde8
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diff --git a/.github/workflows/covr.yml b/.github/workflows/covr.yml
@@ -4,7 +4,7 @@ name: code coverage
 
 on:
   push:
-    branches: [ "dev2 " ]
+    branches: [ "dev2" ]
   schedule:
     - cron: '16 20 * * 2'
 
@@ -37,19 +37,66 @@ jobs:
           install-pandoc: false
           extra-packages: |
             github::drieslab/GiottoData
+            any::covr
             any::rcmdcheck
             any::testthat
             any::rlang
             any::R.utils
+            any::knitr
+            any::rmarkdown
+            any::qs
             any::sp
             any::stars
             any::raster
             any::sf
+            any::scattermore
+            any::exactextractr
             any::RTriangle
             any::geometry
-            any::covr
+            any::qs
+            any::future.apply
+            any::Biobase
+            any::chihaya
+            any::DelayedArray
+            any::DelayedMatrixStats
+            any::HDF5Array
+            any::plotly
+            any::rgl
+            any::rhdf5
+            any::S4Vectors
+            any::ScaledMatrix
+            any::XML
+            any::Seurat
+            any::SeuratObject
+            any::SingleCellExperiment
+            any::SpatialExperiment
+            any::STexampleData
+            any::SummarizedExperiment
+
           needs: coverage
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: setup giotto_env
+        shell: Rscript {0}
+        run: |
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
+          
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
+
       - name: Generate coverage report
         run: |
           covr::codecov(

diff --git a/.github/workflows/dev_check.yml b/.github/workflows/dev_check.yml
@@ -87,24 +87,21 @@ jobs:
       - name: setup giotto_env
         shell: Rscript {0}
         run: |
-          path_to_python <- reticulate::virtualenv_create(
-            envname = "giotto_env",
-            python = Sys.which("python"), # placed on PATH by the setup-python action
-            packages = c(
-              "pandas==1.5.1",
-              "networkx==2.8.8",
-              "python-igraph==0.10.2",
-              "leidenalg==0.9.0", 
-              "python-louvain==0.16",
-              "scikit-learn==1.1.3",
-              "scipy==1.13.0",
-              "scanpy"
-             )
-           )
-              
-           writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
-                      Sys.getenv("GITHUB_ENV"))
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
 
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
+        
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2
         with:

diff --git a/.github/workflows/main_check.yml b/.github/workflows/main_check.yml
@@ -11,7 +11,7 @@ name: R-CMD-check
 
 on:
   pull_request:
-    types: closed
+    types: opened
     branches: [ "main" ]
 
 permissions:
@@ -64,9 +64,9 @@ jobs:
             any::testthat
             any::rlang
             any::R.utils
-            any::remotes
             any::knitr
             any::rmarkdown
+            any::qs
             any::sp
             any::stars
             any::raster
@@ -77,14 +77,46 @@ jobs:
             any::geometry
             any::qs
             any::future.apply
+            any::Biobase
+            any::chihaya
+            any::DelayedArray
+            any::DelayedMatrixStats
+            any::HDF5Array
+            any::plotly
+            any::rgl
+            any::rhdf5
+            any::S4Vectors
+            any::ScaledMatrix
+            any::XML
+            any::Seurat
+            any::SeuratObject
+            any::SingleCellExperiment
+            any::SpatialExperiment
+            any::STexampleData
+            any::SummarizedExperiment
             github::drieslab/GiottoData
 
-      - name: Test python env build
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: setup giotto_env
+        shell: Rscript {0}
         run: |
           if (!GiottoClass::checkGiottoEnvironment()) {
             GiottoClass::installGiottoEnvironment()
           }
-        shell: Rscript {0}
+          
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
 
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2

diff --git a/.gitignore b/.gitignore
@@ -8,5 +8,5 @@ inst/doc
 .Rprofile
 docs
 codecov.yml
-
+pkgdown
 cell_rna*
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.3.2
+Version: 0.3.5
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -24,17 +24,17 @@ Description: This package contains the Giotto object and subobject class
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends:
-    base (>= 4.0.1),
-    utils (>= 4.0.1),
-    R (>= 4.0.1),
+    base (>= 4.4.0),
+    utils (>= 4.4.0),
+    R (>= 4.4.0),
 Imports:
     checkmate,
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     deldir (>= 1.0.6),
-    GiottoUtils (>= 0.1.7),
+    GiottoUtils (>= 0.1.10),
     graphics,
     grDevices,
     igraph (>= 1.2.4.1),
@@ -79,8 +79,7 @@ Suggests:
     SummarizedExperiment,
     testthat (>= 3.0.0),
     qs,
-    XML
-Remotes: drieslab/GiottoUtils
+    xml2
 Config/testthat/edition: 3
 Collate: 
     'package_imports.R'
@@ -107,6 +106,7 @@ Collate:
     'interoperability.R'
     'join.R'
     'methods-IDs.R'
+    'methods-affine.R'
     'methods-centroids.R'
     'methods-coerce.R'
     'methods-copy.R'
@@ -125,6 +125,7 @@ Collate:
     'methods-reconnect.R'
     'methods-rescale.R'
     'methods-setGiotto.R'
+    'methods-shear.R'
     'methods-show.R'
     'methods-spatShift.R'
     'methods-spin.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,affine2d)
 S3method(.DollarNames,dimObj)
 S3method(.DollarNames,metaData)
 S3method(.DollarNames,spatEnrObj)
@@ -8,6 +9,7 @@ S3method(.DollarNames,terraVectData)
 S3method(as.data.table,SpatVector)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
+S3method(print,giottoInstructions)
 S3method(t,spatLocsObj)
 S3method(t,spatialNetworkObj)
 export(addCellMetadata)
@@ -322,6 +324,8 @@ exportMethods("prov<-")
 exportMethods("spatUnit<-")
 exportMethods(activeFeatType)
 exportMethods(activeSpatUnit)
+exportMethods(affine)
+exportMethods(as.character)
 exportMethods(as.matrix)
 exportMethods(as.points)
 exportMethods(as.polygons)
@@ -357,6 +361,7 @@ exportMethods(reconnect)
 exportMethods(rescale)
 exportMethods(rownames)
 exportMethods(setGiotto)
+exportMethods(shear)
 exportMethods(spatIDs)
 exportMethods(spatShift)
 exportMethods(spatUnit)
@@ -405,8 +410,10 @@ importMethodsFrom(terra,as.points)
 importMethodsFrom(terra,as.polygons)
 importMethodsFrom(terra,centroids)
 importMethodsFrom(terra,crop)
+importMethodsFrom(terra,density)
 importMethodsFrom(terra,ext)
 importMethodsFrom(terra,flip)
+importMethodsFrom(terra,hist)
 importMethodsFrom(terra,ncol)
 importMethodsFrom(terra,nrow)
 importMethodsFrom(terra,plot)

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,80 @@
 
-# GiottoClass 0.3.2
+# GiottoClass 0.3.6 (2024/08/30)
+
+## bug fixes
+- fix `dimnames()` for some subobjects
+
+## enhancements
+- python packages to install through pip is now settable in `installGiottoEnvironment()`
+
+# GiottoClass 0.3.5 (2024/08/28)
+
+## breaking changes
+- `set_giotto_python_path()` will now also initialize python env to set by default and print which python env is active, but otherwise do nothing if any python env has already been initialized.
+- deprecated `readGiottoInstructions()`, `showGiottoInstructions()`, `changeGiottoInstructions()`, `replaceGiottoInstructions()` in favor of `instructions()` generic
+
+## bug fixes
+- intensity images now automatically scale to estimated highest value
+- `giottoPolygon` `plot()` default `max_poly` raised to `1e6`
+- `giottoInstructions` no longer lose class when specific params are replaced
+- `ometif_to_tif()` now checks for _imagecodecs_ package as well
+- `anndataToGiotto()` and `giottoToAnndata` now check for _anndata_ package as well.
+- fix `joinGiottoObjects()` `"z_stack"` join method
+- fix error in documentation [#214](https://github.com/drieslab/GiottoClass/issues/214) by shaojunyu
+- fix error in `installGiottoEnvironment()` [#1006](https://github.com/drieslab/Giotto/issues/1006) by 13954380607
+
+## enhancements
+- `print()` method for `giottoInstructions`
+- `rbind()` for `spatLocsObj`
+
+
+# GiottoClass 0.3.4 (2024/08/04)
+
+## bug fixes
+- hotfix anndata matrix support [#216](https://github.com/drieslab/GiottoClass/issues/216) by wwang-chcn
+
+# GiottoClass 0.3.3 (2024/07/29)
+
+## bug fixes
+- fix flipping issue with `giottoAffineImage` for certain affine transforms
+
+## enhancements
+- `missing` method for `affine()` instantiates an `affine2d` object
+
+# GiottoClass 0.3.2 (2024/07/26)
+
+## breaking changes
+- python environment installation and how it relates to default settings such as .condarc may have changed.
+- `giottoImage` `name` slot now requires `character` and will not accept `NULL`
+
+## bug fixes
+- `loadGiotto()` no longer errors with similarly named spat_units or feat_types (e.g. "cell" and "new_cell" would previously throw an error)
+- fix in `giottoToSpatialExperiment()`
+- fix for `giottoToSeuratV5` for cosmx mini dataset [#989](https://github.com/drieslab/Giotto/issues/989) by guillermoturiel
+- fix issue with prints in `createGiottoCosMxObject()` [#960](https://github.com/drieslab/Giotto/issues/960) by GBeattie
 
 ## enhancements
 - `verbose` param for `createNearestNetwork()`
+- `checkGiottoEnvironment()` in addition to full filepaths, also now supports name of environment or installation directory
+- `installGiottoEnvironment()`, `removeGiottoEnvironment()` now have `conda` param for setting path to conda executable and `envname` param for specifying environment by name
+- `installGiottoEnvironment()` now has `confirm` param for skipping path input checks
+- `t()` for `giotto` now affects images as well.
+
+## new
+- `affine()` for `giottoPolygon`, `giottoPoints`, `spatLocsObj`, `giotto`
+- `shear()` for `giottoPoints`, `giottoPolygon`, `spatLocsObj`, `affine2d`
+- `affine2d` class for accumulating linear transforms to be used with `affine()`
+- `initialize()`, `[`, `$`, `show()`, `plot()`, methods for `affine2d`
+- `spin()`, `rescale`, `spatShift()`, `affine()`, `flip()`, `shear()` `t()` methods for `affine2d`
+- `giottoAffineImage` class for just-in-time affine transformed images
+- `initialize()`, method for `giottoLargeImage`
+- `initialize()`, `ext()`, `crop()`, `rescale()`, `spatShift()`, `plot()`, methods for `giottoAffineImage`
+- `rescale()` method for `giottoImage`
+- `spin()`, `shear()`, `affine()`, `flip()`, `t()` methods for `giottoAffineImage` and `giottoLargeImage` (which converts to `giottoAffineImage`)
+- `as()` conversion from `giottoLargeImage` to `giottoAffineImage`
+- `.get_centroid_xy()` internal for getting numeric centroid xy values of any object that responds to `ext()`
+- `.bound_poly()` internal for generating a dummy polygon from the extent of any object that responds to `ext()`
+- `.aff_shift_2d()`, `.aff_shift_2d<-()`, `.aff_linear_2d`, `.aff_linear_2d()<-` internals for accessing and manipulating affine matrices
 
 
 # GiottoClass 0.3.1 (2024/05/21)

diff --git a/R/NN_network.R b/R/NN_network.R
@@ -704,7 +704,7 @@ createNearestNetwork <- function(
                 expression_values
             ))
         )
-        expr_obj <- get_expression_values(
+        expr_obj <- getExpression(
             gobject = gobject,
             feat_type = feat_type,
             spat_unit = spat_unit,

diff --git a/R/aggregate.R b/R/aggregate.R
@@ -1900,7 +1900,7 @@ aggregateStacksExpression <- function(gobject,
     # aggregate matrices
     matrix_list <- list()
     for (spat_unit in spat_units) {
-        mat <- get_expression_values(gobject,
+        mat <- getExpression(gobject,
             spat_unit = spat_unit,
             feat_type = feat_type,
             values = values,