Merge pull request #64 from jiajic/dev

minor: catch up to main

R/interoperability.R

@@ -161,6 +161,7 @@ check_py_for_scanpy = function(){
 #' @param feat_type desired feature type for conversion, default NULL
 #' @param h5_file name to create and on-disk HDF5 file
 #' @param python_path path to python executable within a conda/miniconda environment
+#' @param env_name name of environment containing python_path executable
 #'
 #' @return Giotto object
 #' @details Function in beta. Converts a .h5ad file into a Giotto object.
@@ -174,8 +175,9 @@ anndataToGiotto = function(anndata_path = NULL,
                            deluanay_spat_net = TRUE,
                            spat_unit = NULL,
                            feat_type = NULL,
+                           h5_file = NULL,
                            python_path = NULL,
-                           h5_file = NULL) {
+                           env_name = "giotto_env") {
 
   # Preliminary file checks and guard clauses
   if (is.null(anndata_path)) {
@@ -196,7 +198,8 @@ anndataToGiotto = function(anndata_path = NULL,
   # Required step to properly initialize reticualte
   instrs = createGiottoInstructions(python_path = python_path)
 
-  check_py_for_scanpy()
+  scanpy_installed = checkPythonPackage("scanpy", env_to_use = env_name)
+  # should trigger a stop() downstream if not installed
 
   # Import ad2g, a python module for parsing anndata
   ad2g_path <- system.file("python","ad2g.py",package="Giotto")
@@ -492,6 +495,7 @@ anndataToGiotto = function(anndata_path = NULL,
 #' @param spat_unit spatial unit which will be used in conversion.
 #' @param feat_type feature type which will be used in conversion.
 #' @param python_path path to python executable within a conda/miniconda environment
+#' @param env_name name of environment containing python_path executable
 #' @param save_directory directory in which the file will be saved.
 #' @return vector containing .h5ad file path(s)
 #' @details Function in beta. Converts a Giotto object into .h5ad file(s).
@@ -515,6 +519,7 @@ giottoToAnnData <- function(gobject = NULL,
                             spat_unit = NULL,
                             feat_type = NULL,
                             python_path = NULL,
+                            env_name = "giotto_env",
                             save_directory = NULL){
 
   # Check gobject
@@ -523,6 +528,8 @@ giottoToAnnData <- function(gobject = NULL,
     stop(wrap_msg("Please provide a valid Giotto Object for conversion."))
   }
 
+  scanpy_installed = checkPythonPackage("scanpy", env_to_use = env_name)
+
   # Python module import
   g2ad_path <- system.file("python","g2ad.py",package="Giotto")
   reticulate::source_python(g2ad_path)

R/python_bento.R

@@ -2,9 +2,15 @@
 #' @name createBentoAdata
 #' @description Create bento adata object from gobject
 #' @param gobject Giotto object
+#' @param env_to_use Python environment within which bento is installed.
+#' If it is not already installed, the user
+#' will be prompted to install `bento-tools`
+#' DEFAULT: "giotto_env"
 #' @return bento_adata bento adata object
 #' @export
-createBentoAdata <- function(gobject){
+createBentoAdata <- function(gobject = NULL,
+                             env_to_use = "giotto_env"){
+  if(!c("giotto") %in% class(gobject)) stop(wrap_txt("Please provide a valid Giotto Object.", errWidth=TRUE))
   # Transcripts
   transcripts_df <- as.data.frame(sf::st_as_sf(gobject@feat_info$rna@spatVector))
   coordinates_df <- lapply(transcripts_df['geometry'], sf::st_coordinates)$geometry
@@ -21,6 +27,12 @@ createBentoAdata <- function(gobject){
   nucleus_poly <- spatVector_to_dt(gobject@spatial_info$nucleus@spatVector)
   nucleus_poly <- data.frame(cell_id = nucleus_poly$poly_ID, x = nucleus_poly$x, y = nucleus_poly$y, batch = 0L)
 
+  # Install bento-tools / Check python environment for bento-tools
+  bento_installed = checkPythonPackage(github_package_url = "git+https://github.com/wwang-chcn/bento-tools.git",
+                                       env_to_use = env_to_use)
+  # Will crash downstream if installation unsuccessful/denied 
+  # or if the package is not found.
+
   # Create AnnData object
   g2bento_path <- system.file("python","g2bento.py",package="Giotto")
   reticulate::source_python(g2bento_path)