Merge pull request #149 from omnideconv/fixCI

Fix ci

.github/workflows/test.yml

@@ -48,7 +48,7 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 4.2.2 # ${{ matrix.config.r }}
+          r-version: 4.4.0 # ${{ matrix.config.r }}
           # http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
@@ -73,8 +73,11 @@ jobs:
       - name: Install SpatialExperiment
         run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
 
+      - name: Install Seurat
+        run: Rscript -e "install.packages('Matrix')"
+
       - name: Install Test Dependencies
-        run: Rscript -e "pak::pkg_install(c('testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv', 'satijalab/seurat'))" # drighelli/SpatialExperiment'
+        run: Rscript -e "pak::pkg_install(c('testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv'))" # drighelli/SpatialExperiment'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.gitignore

@@ -7,3 +7,5 @@
 Rplot.png
 /doc/
 /Meta/
+/tests/omnipathr-log/
+.notes

DESCRIPTION

@@ -1,6 +1,7 @@
 Package: spacedeconv
 Title: Unified Interface to spatial transcriptomics deconvolution tools
 Version: 0.1.1
+URL: https://omnideconv.github.io/spacedeconv
 Authors@R: 
     person(given="Constantin", family="Zackl", email="constantin.zackl@student.uibk.ac.at", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1991-6943"))
 Description: Collection of 31 deconvolution tools for spatial transcriptomics data.
@@ -69,7 +70,7 @@ Suggests:
     MuSiC, 
     markdown, 
     EPIC,
-    Seurat,
+    Seurat (<= 4.4.0),
     SeuratObject, 
     plotly, 
     Orthology.eg.db, 

README.md

@@ -101,7 +101,6 @@ cite both our package and the method(s) you are using.
 
 > Constantin Zackl, Maria Zopoglou, Reto Stauffer, Markus Ausserhofer, Marieke E. Ijsselsteijn, Gregor Sturm, Noel Filipe da Cunha Carvalho de Miranda, Francesca Finotello. spacedeconv: deconvolution of tissue architecture from spatial transcriptomics, PREPRINT available at Research Square https://doi.org/10.21203/rs.3.rs-5102166/v1
 
-
 | First-gen (immunedeconv)                                                                                                                                                               | First-gen mouse (immunedeconv)                                            | Second-gen (omnideconv + spatial Methods)                                                                                                                                                                                                                                                           |
 | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | <ul><li>MPCcounter</li><li>EPIC</li><li>quanTIseq</li><li>xCell</li><li>CIBERSORT</li><li>CIBERSORT (abs.)</li><li>TIMER</li><li>ConsensusTME</li><li>ABIS</li><li>ESTIMATE</li> </ul> | <ul> <li>mMCPcounter</li><li>seqImmuCC</li><li>DCP</li><li>BASE</li></ul> | <ul><li>RCTD</li><li>SPOTlight</li><li>CARD</li><li>spatialDWLS</li><li>Cell2location</li><li>AutoGeneS</li><li>BayesPrism</li><li>Bisque</li><li>Bisque</li><li>Bseq-sc</li><li>CIBERSORTx</li><li>CDseq</li><li>CPM</li><li>DWLS</li><li>MOMF</li><li>MuSiC</li><li>Scaden</li><li>SCDC</li></ul> |

_pkgdown.yml

@@ -34,6 +34,7 @@ reference:
   - title: Visualization
     contents:
       - plot_gene
+      - plot_spatial
       - plot_celltype
       - plot_umi_count
       - plot_ndetected_genes

tests/testthat/test-python.R

@@ -8,9 +8,5 @@ test_that("Python environment creation works", {
   expect_true(reticulate::py_module_available("leidenalg"))
   expect_true(reticulate::py_module_available("community")) # python louvain
   expect_true(reticulate::py_module_available("sklearn"))
-  # expect_true(reticulate::py_module_available("python.app"))
   expect_true(reticulate::py_module_available("scanpy"))
-  expect_true(reticulate::py_module_available("cell2location"))
-  # expect_true(reticulate::py_module_available("metacells"))
-  expect_true(reticulate::py_module_available("autogenes"))
 })

tests/testthat/test-signature.R

@@ -35,16 +35,3 @@ test_that("build_model requires supported method", {
 test_that("deconvolute requires non-null spatial_obj", {
   expect_error(deconvolute(NULL), "Parameter 'spatial_obj' is missing or null, but is required.")
 })
-
-test_that("Second-gen signature creation with SCDC works", {
-  signature <- build_model(sce, cell_type_col = "celltype_major", method = "scdc", verbose = T, batch_id_col = "orig.ident")
-  expect_equal(ncol(signature), expected = 4)
-  expect_type(signature, "double")
-})
-
-
-test_that("Second-gen deconvolution with SCDC works", {
-  deconv <- deconvolute(spe, signature, method = "scdc", single_cell_obj = sce, cell_type_col = "celltype_major", batch_id_col = "orig.ident")
-  expect_true("scdc_Endothelial" %in% colnames(colData(deconv)))
-  expect_s4_class(deconv, "SpatialExperiment")
-})