!feat: remove combineSpatialCellFeatureInfo()

- function does not work and is not used anywhere

NAMESPACE

@@ -53,7 +53,6 @@ export(combineCellData)
 export(combineFeatureData)
 export(combineFeatureOverlapData)
 export(combineMetadata)
-export(combineSpatialCellFeatureInfo)
 export(combineSpatialCellMetadataInfo)
 export(combineToMultiPolygon)
 export(compatible_spatial_network)

R/combine_metadata.R

@@ -90,86 +90,6 @@ combineMetadata <- function(
 
 
 
-#' @title combineSpatialCellFeatureInfo
-#' @name combineSpatialCellFeatureInfo
-#' @description Combine spatial cell information (e.g. polygon)
-#' and spatial feature information (e.g. transcript locations)
-#' @param gobject Giotto object
-#' @param spat_unit spatial unit
-#' @param feat_type feature type(s)
-#' @param selected_features select set of features
-#' @returns list of data.table(s)
-#' @details
-#' The returned data.table has the following columns: \cr
-#' \itemize{
-#'   \item{sdimx: spatial feature location on the x-axis}
-#'   \item{sdimy: spatial feature location on the y-axis}
-#'   \item{feat_ID: unique feature ID}
-#'   \item{cell_ID: unique cell ID}
-#'   \item{used: how often was the feature used/assigned to a cell}
-#'   \item{feat: selected feature(s)}
-#' }
-#'
-#' @export
-combineSpatialCellFeatureInfo <- function(
-        gobject,
-        spat_unit = NULL,
-        feat_type = NULL,
-        selected_features = NULL) {
-    # define for data.table
-    feat_ID <- NULL
-
-    # combine
-    # 1. spatial morphology information ( = polygon)
-    # 2. spatial transcript location information
-
-    # Set feat_type and spat_unit
-    spat_unit <- set_default_spat_unit(
-        gobject = gobject,
-        spat_unit = spat_unit
-    )
-    feat_type <- set_default_feat_type(
-        gobject = gobject,
-        spat_unit = spat_unit,
-        feat_type = feat_type
-    )
-
-    spatial_cell_info <- gobject@spatial_info
-
-    if (is.null(spatial_cell_info)) {
-        stop("There is no available spatial segmentation/location information")
-    }
-
-
-    res_list <- list()
-    for (feat in unique(feat_type)) {
-        spatial_feat_locs <- gobject@feat_info[[feat]]
-
-        if (!is.null(selected_features)) {
-            spatial_feat_locs <- spatial_feat_locs[
-                feat_ID %in% selected_features
-            ]
-        }
-
-        if (is.null(spatial_feat_locs)) {
-            stop("There is no available spatial feature location information
-                for ", feat, "\n")
-        }
-
-        output <- .merge_spatial_locs_feat_info(
-            spatial_info = spatial_cell_info,
-            feature_info = spatial_feat_locs
-        )
-        output[, "feat" := feat]
-
-        res_list[[feat]] <- output
-    }
-
-    return(res_list)
-}
-
-
-
 #' @title combineSpatialCellMetadataInfo
 #' @name combineSpatialCellMetadataInfo
 #' @description Combine cell metadata with spatial cell
@@ -738,46 +658,6 @@ calculateSpatCellMetadataProportions <- function(
 
 # internals ####
 
-#' @title .merge_spatial_locs_feat_info
-#' @name .merge_spatial_locs_feat_info
-#' @returns data.table
-#' @description merge spatial cell and feature location information
-#' @keywords internal
-#' @noRd
-.merge_spatial_locs_feat_info <- function(
-        spatial_info,
-        feature_info) {
-    # data.table variables
-    cell_ID <- used <- NULL
-
-    reslist <- list()
-    for (i in seq_len(length(unique(spatial_info$cell_ID)))) {
-        cell_i <- unique(spatial_info$cell_ID)[i]
-
-        temp <- sp::point.in.polygon(
-            point.x = feature_info$sdimx,
-            point.y = feature_info$sdimy,
-            pol.x = spatial_info[cell_ID == cell_i]$sdimx,
-            pol.y = spatial_info[cell_ID == cell_i]$sdimy
-        )
-
-        detected_feats <- feature_info[temp == 1]
-        detected_feats[, cell_ID := cell_i]
-
-        reslist[[i]] <- detected_feats
-    }
-
-    reslistfinal <- do.call("rbind", reslist)
-
-    # calculate how often a single transcript is used
-    # > 1 means that a transcript was assigned to more than 1 cell
-    reslistfinal[, used := .N, by = c("sdimx", "sdimy", "feat_ID")]
-
-    return(reslistfinal)
-}
-
-
-
 
 
 #' @title .merge_spatial_enrich_info