Merge pull request #93 from drieslab/dev

Fix overlapToMatrix()
drieslab · Nov 19, 2023 · c6b3bd3 · c6b3bd3
2 parents 912f3c1 + 1db5c1e
commit c6b3bd3
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Showing 10 changed files with 766 additions and 759 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,6 +45,7 @@ Imports:
     terra (>= 1.7-39)
 Suggests: 
     Biobase,
+    chihaya,
     DelayedArray,
     exactextractr,
     geometry,

diff --git a/R/aggregate.R b/R/aggregate.R
@@ -1060,8 +1060,8 @@ setMethod(
   'overlapToMatrix', signature('giotto'), function(
     x,
     name = 'raw',
-    poly_info = 'cell',
-    feat_info = 'rna',
+    poly_info = NULL,
+    feat_info = NULL,
     type = c('point', 'intensity'),
     count_info_column = NULL,
     aggr_function = "sum",
@@ -1070,26 +1070,33 @@ setMethod(
     ...
   )
   {
+
     type = match.arg(type, choices = c('point', 'intensity'))
     checkmate::assert_character(name, len = 1L)
-    checkmate::assert_character(poly_info, len = 1L)
-    checkmate::assert_character(feat_info, len = 1L)
     if (!is.null(count_info_column)) {
       checkmate::assert_character(count_info_column, len = 1L)
     }
     checkmate::assert_logical(return_gobject)
 
+    poly_info <- set_default_spat_unit(gobject = x,
+                                       spat_unit = poly_info)
+    feat_info <- set_default_feat_type(gobject = x,
+                                       spat_unit = poly_info,
+                                       feat_type = feat_info)
+
     # get data
     gpoly = getPolygonInfo(
       gobject = x,
       polygon_name = poly_info,
-      return_giottoPolygon = TRUE
+      return_giottoPolygon = TRUE,
+      verbose = verbose
     )
 
     o2m_args <- list(
       x = gpoly,
       col_names = spatIDs(x, spat_unit = poly_info),
       row_names = featIDs(x, feat_type = feat_info),
+      feat_info = feat_info,
       count_info_column = count_info_column,
       aggr_function = aggr_function,
       # output = 'Matrix', # Do not specify here. methods must return
@@ -1237,7 +1244,7 @@ setMethod(
     # 2. Perform aggregation to counts DT
     if(!is.null(count_info_column)) { # if there is a counts col
 
-      if(!count_info_column %in% colnames(dtoverlap)) {
+      if (!count_info_column %in% colnames(dtoverlap)) {
         stop('count_info_column ', count_info_column, ' does not exist')
       }
 

diff --git a/R/generics.R b/R/generics.R
@@ -6,8 +6,8 @@ NULL
 
 # Giotto Object Settings ####
 # Methods and documentations found in methods-IDs.R
-setGeneric('spatIDs', function(x, spat_unit, ...) standardGeneric('spatIDs'))
-setGeneric('featIDs', function(x, feat_type, ...) standardGeneric('featIDs'))
+setGeneric('spatIDs', function(x, ...) standardGeneric('spatIDs'))
+setGeneric('featIDs', function(x, ...) standardGeneric('featIDs'))
 
 ## instructions ####
 # Methods and documentations found in methods-instructions.R

diff --git a/R/methods-IDs.R b/R/methods-IDs.R
@@ -27,74 +27,69 @@ NULL
 
 # spatIDs ####
 
+
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = 'giotto', spat_unit = 'missing'),
-          function(x, ...) {
-            as.character(get_cell_id(gobject = x, ...))
-          })
-#' @rdname spatIDs-generic
-#' @export
-setMethod('spatIDs', signature(x = 'giotto', spat_unit = 'character'),
-          function(x, spat_unit, ...) {
+setMethod('spatIDs', signature(x = 'giotto'),
+          function(x, spat_unit = NULL, ...) {
             as.character(get_cell_id(gobject = x, spat_unit, ...))
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = c('exprObj'), spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = c('exprObj')),
           function(x, ...) {
             as.character(colnames(x[]))
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = c('spatLocsObj'), spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = c('spatLocsObj')),
           function(x, ...) {
             as.character(x[]$cell_ID)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = c('cellMetaObj'), spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = c('cellMetaObj')),
           function(x, ...) {
             as.character(x[]$cell_ID)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = c('spatialNetworkObj'), spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = c('spatialNetworkObj')),
           function(x, ...) {
             as.character(unique(c(x[]$from, x[]$to)))
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = 'dimObj', spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = 'dimObj'),
           function(x, ...) {
             as.character(rownames(x@coordinates))
           })
 #' @rdname spatIDs-generic
 #' @param use_cache use cached IDs if available (gpoly and gpoints only)
 #' @param uniques return unique ID values only (currently gpoly and gpoints only)
 #' @export
-setMethod('spatIDs', signature(x = 'giottoPolygon', spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = 'giottoPolygon'),
           function(x, use_cache = TRUE, uniques = TRUE, ...) {
             if (!all(is.na(x@unique_ID_cache)) &&
                 isTRUE(use_cache) &&
                 isTRUE(uniques)) {
               return(as.character(x@unique_ID_cache))
             }
-            
+
             # getting as list first is more performant
             out = as.character(terra::as.list(x@spatVector)$poly_ID)
             if (isTRUE(uniques)) out = unique(out)
             return(out)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = 'spatEnrObj', spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = 'spatEnrObj'),
           function(x, ...) {
             as.character(x@enrichDT$cell_ID)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('spatIDs', signature(x = 'nnNetObj', spat_unit = 'missing'),
+setMethod('spatIDs', signature(x = 'nnNetObj'),
           function(x, ...) {
             as.character(unique(names(igraph::V(x@igraph))))
           })
@@ -106,48 +101,43 @@ setMethod('spatIDs', signature(x = 'nnNetObj', spat_unit = 'missing'),
 
 # featIDs ####
 
+
 #' @rdname spatIDs-generic
 #' @export
-setMethod('featIDs', signature(x = 'giotto', feat_type = 'missing'),
-          function(x, ...) {
-            as.character(get_feat_id(gobject = x, ...))
-          })
-#' @rdname spatIDs-generic
-#' @export
-setMethod('featIDs', signature(x = 'giotto', feat_type = 'character'),
-          function(x, feat_type, ...) {
+setMethod('featIDs', signature(x = 'giotto'),
+          function(x, feat_type = NULL, ...) {
             as.character(get_feat_id(gobject = x, feat_type, ...))
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('featIDs', signature(x = 'exprObj', feat_type = 'missing'),
+setMethod('featIDs', signature(x = 'exprObj'),
           function(x, ...) {
             as.character(rownames(x[]))
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('featIDs', signature(x = 'featMetaObj', feat_type = 'missing'),
+setMethod('featIDs', signature(x = 'featMetaObj'),
           function(x, ...) {
             as.character(x[]$feat_ID)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('featIDs', signature(x = 'giottoPoints', feat_type = 'missing'),
+setMethod('featIDs', signature(x = 'giottoPoints'),
           function(x, use_cache = TRUE, uniques = TRUE, ...) {
             if (!all(is.na(x@unique_ID_cache)) &&
                 isTRUE(use_cache) &&
                 isTRUE(uniques)) {
               return(as.character(x@unique_ID_cache))
             }
-            
+
             # getting as list is more performant than directly using `$`
             out = as.character(terra::as.list(x@spatVector)$feat_ID)
             if (isTRUE(uniques)) out = unique(out)
             return(out)
           })
 #' @rdname spatIDs-generic
 #' @export
-setMethod('featIDs', signature(x = 'spatEnrObj', feat_type = 'missing'),
+setMethod('featIDs', signature(x = 'spatEnrObj'),
           function(x, ...) {
             as.character(colnames(x@enrichDT[, -'cell_ID']))
           })

diff --git a/R/methods-ext.R b/R/methods-ext.R
@@ -72,7 +72,8 @@ setMethod('ext<-', signature(x = 'giottoPolygon', value = 'SpatExtent'), functio
 #' @rdname ext-generic
 #' @export
 setMethod('ext<-', signature(x = 'giottoLargeImage', value = 'SpatExtent'), function(x, value) {
-  terra::ext(x@raster_object) = value
+  terra::ext(x@raster_object) <- value
+  x@extent <- value
   x
 })