Fix Bioc review issues (#372)

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

Author: lazappi

.Rbuildignore

@@ -15,3 +15,4 @@
 ^doc$
 ^Meta$
 ^man/figures/*\.svg$
+^data$

.gitignore

@@ -60,3 +60,4 @@ rsconnect/
 vignettes/data/*.h5ad
 /doc/
 /Meta/
+/data/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 0.99.5
+Version: 0.99.6
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "robrecht@data-intuitive.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),

NEWS.md

@@ -1,3 +1,10 @@
+# anndataR 0.99.6
+
+- Use the correct mapping figure in the `SingleCellExperiment` usage vignette (PR #372)
+- Fix accessing layers keys for `ReticulateAnnData` (PR #372)
+- Minor updates to the Python usage vignette (PR #372)
+- Add the Python vignette to the **{pkgdown}** index (PR #372)
+
 # anndataR 0.99.4
 
 - Address minor issues from Bioconductor checks (PR #371)

R/ReticulateAnnData.R

@@ -34,7 +34,7 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_X, status=done
-        py_to_r(private$.py_anndata$X)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "X"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_X, status=done
         value <- private$.validate_aligned_array(
@@ -44,7 +44,7 @@ ReticulateAnnData <- R6::R6Class(
           expected_rownames = rownames(self),
           expected_colnames = colnames(self)
         )
-        private$.py_anndata$X <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "X", r_to_py(value))
         self
       }
     },
@@ -57,9 +57,15 @@ ReticulateAnnData <- R6::R6Class(
         # trackstatus: class=ReticulateAnnData, feature=get_layers, status=done
         bi <- reticulate::import_builtins()
         out <- list()
-        keys <- bi$list(private$.py_anndata$layers$keys())
+        keys <- bi$list(reticulate::py_get_attr(
+          private$.py_anndata,
+          "layers"
+        )$keys())
         for (name in keys) {
-          out[[name]] <- py_to_r(private$.py_anndata$layers[[name]])
+          out[[name]] <- py_to_r(reticulate::py_get_attr(
+            private$.py_anndata,
+            "layers"
+          )[[name]])
         }
         out
       } else {
@@ -71,7 +77,7 @@ ReticulateAnnData <- R6::R6Class(
           expected_rownames = rownames(self),
           expected_colnames = colnames(self)
         )
-        private$.py_anndata$layers <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "layers", r_to_py(value))
         self
       }
     },
@@ -82,11 +88,11 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_obs, status=done
-        py_to_r(private$.py_anndata$obs)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "obs"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_obs, status=done
         value <- private$.validate_obsvar_dataframe(value, "obs")
-        private$.py_anndata$obs <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "obs", r_to_py(value))
         self
       }
     },
@@ -97,11 +103,11 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_var, status=done
-        py_to_r(private$.py_anndata$var)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "var"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_var, status=done
         value <- private$.validate_obsvar_dataframe(value, "var")
-        private$.py_anndata$var <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "var", r_to_py(value))
         self
       }
     },
@@ -113,10 +119,17 @@ ReticulateAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_obs_names, status=done
         bi <- reticulate::import_builtins()
-        reticulate::py_to_r(bi$list(private$.py_anndata$obs_names))
+        reticulate::py_to_r(bi$list(reticulate::py_get_attr(
+          private$.py_anndata,
+          "obs_names"
+        )))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_obs_names, status=done
-        private$.py_anndata$obs_names <- reticulate::r_to_py(value)
+        reticulate::py_set_attr(
+          private$.py_anndata,
+          "obs_names",
+          reticulate::r_to_py(value)
+        )
         self
       }
     },
@@ -128,10 +141,17 @@ ReticulateAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_var_names, status=done
         bi <- reticulate::import_builtins()
-        reticulate::py_to_r(bi$list(private$.py_anndata$var_names))
+        reticulate::py_to_r(bi$list(reticulate::py_get_attr(
+          private$.py_anndata,
+          "var_names"
+        )))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_var_names, status=done
-        private$.py_anndata$var_names <- reticulate::r_to_py(value)
+        reticulate::py_set_attr(
+          private$.py_anndata,
+          "var_names",
+          reticulate::r_to_py(value)
+        )
         self
       }
     },
@@ -142,7 +162,7 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_obsm, status=done
-        py_to_r(private$.py_anndata$obsm)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "obsm"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_obsm, status=done
         value <- private$.validate_aligned_mapping(
@@ -151,7 +171,7 @@ ReticulateAnnData <- R6::R6Class(
           c(self$n_obs()),
           expected_rownames = rownames(self)
         )
-        private$.py_anndata$obsm <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "obsm", r_to_py(value))
         self
       }
     },
@@ -162,7 +182,7 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_varm, status=done
-        py_to_r(private$.py_anndata$varm)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "varm"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_varm, status=done
         value <- private$.validate_aligned_mapping(
@@ -171,7 +191,7 @@ ReticulateAnnData <- R6::R6Class(
           c(self$n_vars()),
           expected_rownames = colnames(self)
         )
-        private$.py_anndata$varm <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "varm", r_to_py(value))
         self
       }
     },
@@ -182,7 +202,7 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_obsp, status=done
-        py_to_r(private$.py_anndata$obsp)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "obsp"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_obsp, status=done
         value <- private$.validate_aligned_mapping(
@@ -192,7 +212,7 @@ ReticulateAnnData <- R6::R6Class(
           expected_rownames = rownames(self),
           expected_colnames = rownames(self)
         )
-        private$.py_anndata$obsp <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "obsp", r_to_py(value))
         self
       }
     },
@@ -203,7 +223,7 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_varp, status=done
-        py_to_r(private$.py_anndata$varp)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "varp"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_varp, status=done
         value <- private$.validate_aligned_mapping(
@@ -213,7 +233,7 @@ ReticulateAnnData <- R6::R6Class(
           expected_rownames = colnames(self),
           expected_colnames = colnames(self)
         )
-        private$.py_anndata$varp <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "varp", r_to_py(value))
         self
       }
     },
@@ -224,11 +244,11 @@ ReticulateAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ReticulateAnnData, feature=get_uns, status=done
-        py_to_r(private$.py_anndata$uns)
+        py_to_r(reticulate::py_get_attr(private$.py_anndata, "uns"))
       } else {
         # trackstatus: class=ReticulateAnnData, feature=set_uns, status=done
         value <- private$.validate_named_list(value, "uns")
-        private$.py_anndata$uns <- r_to_py(value)
+        reticulate::py_set_attr(private$.py_anndata, "uns", r_to_py(value))
         self
       }
     }
@@ -380,13 +400,19 @@ ReticulateAnnData <- R6::R6Class(
     #' @description See the `n_obs` field in [AnnData-usage]
     n_obs = function() {
       private$.check_py_object_valid()
-      as.integer(reticulate::py_to_r(private$.py_anndata$n_obs))
+      as.integer(reticulate::py_to_r(reticulate::py_get_attr(
+        private$.py_anndata,
+        "n_obs"
+      )))
     },
 
     #' @description See the `n_vars` field in [AnnData-usage]
     n_vars = function() {
       private$.check_py_object_valid()
-      as.integer(reticulate::py_to_r(private$.py_anndata$n_vars))
+      as.integer(reticulate::py_to_r(reticulate::py_get_attr(
+        private$.py_anndata,
+        "n_vars"
+      )))
     },
 
     #' @description Get the underlying Python AnnData object

_pkgdown.yml

@@ -13,6 +13,8 @@ navbar:
       href: articles/usage_seurat.html
     - text: Read/write SingleCellExperiment objects
       href: articles/usage_singlecellexperiment.html
+    - text: Interact with Python AnnData objects
+      href: articles/usage_python.html
     - text: -------
     - text: Development
     - text: Software design

man/figures/AnnData-SCE.png

@@ -10,10 +10,10 @@ vignette: >
 
 ```{r, include = FALSE}
 reticulate::py_require("mudata")
+reticulate::py_require("scanpy")
 
 # Check if required Python packages are available
-python_available <- reticulate::py_available() &&
-  reticulate::py_module_available("scanpy") &&
+python_available <- reticulate::py_module_available("scanpy") &&
   reticulate::py_module_available("mudata")
 
 knitr::opts_chunk$set(
@@ -22,17 +22,19 @@ knitr::opts_chunk$set(
   # Set eval based on Python package availability
   eval = python_available
 )
-
-if (!python_available) {
-  message("Python packages scanpy and mudata are required to run this vignette. Code chunks will not be evaluated.")
-}
 ```
 
 # Introduction
 
 `r Biocpkg("anndataR")` works with Python `AnnData` objects through `r CRANpkg("reticulate")`.
 You can load Python objects, apply Python functions to them, and convert them to `Seurat` or `SingleCellExperiment` objects.
 
+```{r python_unavailable, eval=!python_available}
+message(
+  "Python packages scanpy and mudata are required to run this vignette. Code chunks will not be evaluated."
+)
+```
+
 ## Prerequisites
 
 This vignette requires Python with the _scanpy_ and _mudata_ packages installed.
@@ -43,7 +45,7 @@ If these are not available, the code chunks will not be evaluated but the exampl
 Install required Python packages if needed:
 
 ```{r python_setup, eval=FALSE}
-reticulate::py_install("scanpy")
+reticulate::py_require("scanpy")
 ```
 
 ```{r load_libraries}
@@ -56,7 +58,7 @@ Load a dataset directly from _scanpy_:
 
 ```{r load_python_data}
 adata <- sc$datasets$pbmc3k_processed()
-print(adata)
+adata
 ```
 
 Apply _scanpy_ functions directly:
@@ -73,14 +75,14 @@ Convert to `SingleCellExperiment` (see `vignette("usage_singlecellexperiment")`)
 
 ```{r convert_to_sce}
 sce_obj <- adata$as_SingleCellExperiment()
-print(sce_obj)
+sce_obj
 ```
 
 Convert to `Seurat` (see `vignette("usage_seurat")`):
 
 ```{r convert_to_seurat}
 seurat_obj <- adata$as_Seurat()
-print(seurat_obj)
+seurat_obj
 ```
 
 # Multi-modal data with _mudata_