@@ -22,8 +22,10 @@

 #'   over

 #'

 #' @examples

+#' ## Mock up a SpatialExperiment object wit 400 cells and 3 genes

 #' set.seed(42)

-#' mock <- mockSVG(size = 10, tot_genes = 500, de_genes = 10)

+#' mock <- mockSVG(size = 20, tot_genes = 3, de_genes = 1)

+#'

 #' stabilized <- stabilize(mock$counts)

 #' sample_info <- mock$coordinates

 #' sample_info$total_counts <- colSums(mock$counts)

@@ -49,7 +49,7 @@ run <- function(x, coordinates, verbose = FALSE) {

     proc <- basiliskStart(spatialDE_env, testload="scipy.optimize")

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_run(proc, x, coordinates)

     out <- basiliskRun(proc, function(store) {

@@ -40,29 +40,40 @@

 #' @export

 #' @importFrom checkmate assert_data_frame assert_names assert_matrix

 #' @importFrom checkmate assert_flag

+#' @importFrom basilisk basiliskStart basiliskRun

 run <- function(x, coordinates, verbose = FALSE) {

     assert_data_frame(coordinates, any.missing = FALSE)

     assert_names(colnames(coordinates), identical.to = c("x", "y"))

     assert_matrix(x, any.missing = FALSE)

     assert_flag(verbose)

-

-    out <- basilisk::basiliskRun(

-        env = spatialDE_env,

-        fun = .spatialDE_run,

-        x = x,

-        coordinates = coordinates,

-        verbose = verbose

-    )

+    

+    proc <- basiliskStart(spatialDE_env, testload="scipy.optimize")

+    

+    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .spatialDE_run(proc, x, coordinates)

+    

+    out <- basiliskRun(proc, function(store) {

+        as.data.frame(store$de_results)

+    }, persist=TRUE)

+    

     out

+

 }

 #' @importFrom reticulate r_to_py

-.spatialDE_run <- function(x, coordinates, verbose) {

-    spatialDE <- .importPyModule(!verbose)

-

-    X <- r_to_py(coordinates)

-    ## Need to transpose counts for `spatialDE$run`

-    res_py <- r_to_py(as.data.frame(t(x)))

-

-    spatialDE$run(X, res_py)

+#' @importFrom basilisk basiliskRun

+.spatialDE_run <- function(proc, x, coordinates) {

+    basiliskRun(proc, function(x, coordinates, store) {

+        spatialDE <- store$spatialDE

+        

+        X <- r_to_py(coordinates)

+        ## Need to transpose counts for `spatialDE$run`

+        res_py <- r_to_py(as.data.frame(t(x)))

+        

+        de_results <- spatialDE$run(X, res_py)

+        

+        store$de_results <- as.data.frame(de_results)

+        

+        invisible(NULL)

+    }, x=x, coordinates=coordinates, persist=TRUE)

 }

@@ -1,5 +1,3 @@

-# TODO: add more details regarding DE results format in @return

-

 #' Perform SpatialDE test

 #'

 #' Wraps the `run` function from the

@@ -11,7 +9,17 @@

 #' Each row is a sample, the columns with coordinates must be named 'x' and 'y'.

 #' @param verbose `logical` controlling the display of the progress bar.

 #'

-#' @return `data.frame` with DE results.

+#' @return A `data.frame` with DE results where each row is a gene and columns

+#'   contain relevant statistics.

+#'

+#'   The most important columns are:

+#'

+#'   * `g`: the name of the gene

+#'   * `pval`: the p-value for spatial differential expression

+#'   * `qval`: the q-value, indicating significance after correcting for

+#'   multiple testing

+#'   * `l`: A parameter indicating the distance scale a gene changes expression

+#'   over

 #'

 #' @examples

 #' set.seed(42)

new file mode 100644

@@ -0,0 +1,60 @@

+# TODO: add more details regarding DE results format in @return

+

+#' Perform SpatialDE test

+#'

+#' Wraps the `run` function from the

+#' [SpatialDE](https://github.com/Teichlab/SpatialDE) Python package.

+#'

+#' @param x `matrix`-like object of normalized counts. E.g. resulting from

+#'          [regress_out()].

+#' @param coordinates `data.frame` with sample coordinates.

+#' Each row is a sample, the columns with coordinates must be named 'x' and 'y'.

+#' @param verbose `logical` controlling the display of the progress bar.

+#'

+#' @return `data.frame` with DE results.

+#'

+#' @examples

+#' set.seed(42)

+#' mock <- mockSVG(size = 10, tot_genes = 500, de_genes = 10)

+#' stabilized <- stabilize(mock$counts)

+#' sample_info <- mock$coordinates

+#' sample_info$total_counts <- colSums(mock$counts)

+#' regressed <- regress_out(counts = stabilized, sample_info = sample_info)

+#'

+#' ## Run SpatialDE

+#' de_results <- run(regressed, coordinates = mock$coordinates)

+#'

+#' @references

+#' Svensson, V., Teichmann, S. & Stegle, O.

+#' SpatialDE: identification of spatially variable genes.

+#' Nat Methods 15, 343–346 (2018). \url{https://doi.org/10.1038/nmeth.4636}

+#'

+#' @export

+#' @importFrom checkmate assert_data_frame assert_names assert_matrix

+#' @importFrom checkmate assert_flag

+run <- function(x, coordinates, verbose = FALSE) {

+    assert_data_frame(coordinates, any.missing = FALSE)

+    assert_names(colnames(coordinates), identical.to = c("x", "y"))

+    assert_matrix(x, any.missing = FALSE)

+    assert_flag(verbose)

+

+    out <- basilisk::basiliskRun(

+        env = spatialDE_env,

+        fun = .spatialDE_run,

+        x = x,

+        coordinates = coordinates,

+        verbose = verbose

+    )

+    out

+}

+

+#' @importFrom reticulate r_to_py

+.spatialDE_run <- function(x, coordinates, verbose) {

+    spatialDE <- .importPyModule(!verbose)

+

+    X <- r_to_py(coordinates)

+    ## Need to transpose counts for `spatialDE$run`

+    res_py <- r_to_py(as.data.frame(t(x)))

+

+    spatialDE$run(X, res_py)

+}