@@ -16,7 +16,6 @@ import(methods)

 importFrom(Matrix,colSums)

 importFrom(SpatialExperiment,"spatialCoordsNames<-")

 importFrom(SpatialExperiment,spatialCoords)

-importFrom(SpatialExperiment,spatialCoordsNames)

 importFrom(SummarizedExperiment,assay)

 importFrom(basilisk,BasiliskEnvironment)

 importFrom(checkmate,assert_data_frame)

@@ -1,6 +1,6 @@

-#' Classify SVGenes to interpretable fitting classes

+#' Classify Spatially Variable Genes to interpretable fitting classes

 #'

-#' Compare model fits with different models. 

+#' Compare model fits with different models, using the

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

 #'

 #' @param x \linkS4class{SpatialExperiment} object.

@@ -24,12 +24,13 @@

 #'

 #' ## Run spatialDE with S4 integration

 #' de_results <- spatialDE(spe)

-#' 

+#'

 #' ## Run model search with S4 integration

-#' model_search <- modelSearch(spe, assay_type = "counts", 

-#' de_results = de_results, qval_thresh = NULL, verbose = FALSE)

-#' 

-#' 

+#' model_search <- modelSearch(spe, de_results = de_results,

+#'     qval_thresh = NULL, verbose = FALSE

+#' )

+#'

+#'

 #' @seealso

 #' The individual steps performed by this function: [stabilize()],

 #' [regress_out()] and [model_search()].

@@ -43,21 +44,21 @@

 #' of the Python package used under the hood.

 #'

 #' @author Davide Corso, Milan Malfait

-#' @name model-search

+#' @name modelSearch

 NULL

 #' @importFrom Matrix colSums

-.modelSearch <- function(counts_spe, coordinates_spe, de_results, 

+.modelSearch <- function(counts_spe, coordinates_spe, de_results,

                          verbose = FALSE) {

   sample_info <- data.frame(coordinates_spe, total_counts = colSums(counts_spe))

-  

+

   out <- basilisk::basiliskRun(

-    env = spatialDE_env,

-    fun = .run_model_search,

-    counts_spe=counts_spe, 

-    sample_info=sample_info, 

-    de_results=de_results,

-    verbose=verbose

+      env = spatialDE_env,

+      fun = .run_model_search,

+      counts_spe = counts_spe,

+      sample_info = sample_info,

+      de_results = de_results,

+      verbose = verbose

   )

   out

 }

@@ -67,44 +68,46 @@ NULL

   ## Normalization

   stabilized <- .naiveDE_stabilize(counts = counts_spe)

   regressed <- .naiveDE_regress_out(counts = stabilized, sample_info)

-  

+

   coordinates <- sample_info[, c("x", "y")]

-  .spatialDE_model_search(x = regressed, coordinates = coordinates,

-                          de_results = de_results, verbose = verbose)

+  .spatialDE_model_search(

+      x = regressed, coordinates = coordinates,

+      de_results = de_results, verbose = verbose

+  )

 }

-#' 

 #' @import methods

 #' @export

-#' @rdname model-search

-setGeneric("modelSearch", function(x, ...) 

-  standardGeneric("modelSearch"))

+#' @rdname modelSearch

+setGeneric("modelSearch", function(x, ...) standardGeneric("modelSearch"))

 #' @export

-#' @rdname model-search

+#' @rdname modelSearch

 #' @importFrom SummarizedExperiment assay

-#' @importFrom SpatialExperiment spatialCoords spatialCoordsNames

+#' @importFrom SpatialExperiment spatialCoords spatialCoordsNames<-

 #' @importFrom checkmate assert_data_frame assert_number assert_flag

 setMethod("modelSearch", "SpatialExperiment",

-  function(x, assay_type = "counts", de_results, qval_thresh=0.05, 

+  function(x, assay_type = "counts", de_results, qval_thresh=0.05,

            verbose = FALSE) {

     assert_data_frame(de_results, all.missing = FALSE)

     assert_number(qval_thresh, null.ok = TRUE)

     assert_flag(verbose)

-    

+

     ## Rename spatialCoords columns to "x", "y"

     spatialCoordsNames(x) <- c("x", "y")

     coordinates_spe <- as.data.frame(spatialCoords(x))

     counts_spe <- assay(x, assay_type)

-    

+

     ## Filter de_results

     if (!is.null(qval_thresh)) {

       de_results <- .filter_de_results(

         de_results = de_results, qval_thresh = qval_thresh

       )

     }

-    

-    .modelSearch(counts_spe=counts_spe, coordinates_spe=coordinates_spe,

-                 de_results=de_results, verbose = FALSE)

+

+    .modelSearch(

+        counts_spe = counts_spe, coordinates_spe = coordinates_spe,

+        de_results = de_results, verbose = FALSE

+    )

   }

 )

similarity index 88%

rename from man/model-search.Rd

rename to man/modelSearch.Rd

@@ -1,10 +1,9 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/msearch.R

-\name{model-search}

-\alias{model-search}

+\name{modelSearch}

 \alias{modelSearch}

 \alias{modelSearch,SpatialExperiment-method}

-\title{Classify SVGenes to interpretable fitting classes}

+\title{Classify Spatially Variable Genes to interpretable fitting classes}

 \usage{

 modelSearch(x, ...)

@@ -37,7 +36,7 @@ Python package.}

 \code{data.frame} of model_search results.

 }

 \description{

-Compare model fits with different models.

+Compare model fits with different models, using the

 \href{https://github.com/Teichlab/SpatialDE}{\strong{SpatialDE}} Python package.

 }

 \examples{

@@ -49,8 +48,9 @@ spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE)

 de_results <- spatialDE(spe)

 ## Run model search with S4 integration

-model_search <- modelSearch(spe, assay_type = "counts", 

-de_results = de_results, qval_thresh = NULL, verbose = FALSE)

+model_search <- modelSearch(spe, de_results = de_results,

+    qval_thresh = NULL, verbose = FALSE

+)

 }