Merge pull request drieslab#929 from drieslab/suite_dev

v4.0.5

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.4
+Version: 4.0.5
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),

NEWS.md

@@ -1,5 +1,12 @@
+# Giotto 4.0.5 (2024/03/12)
 
-# Giotto 4.0.4
+## Bug fixes
+* Fix Error "cannot coerce class ‘structure("spatLocsObj", package = "Giotto")’ to a data.frame" in `spatialDE()`
+
+## Enhancements
+* `readPolygonVizgenParquet()` now has `calc_centroids = TRUE` by default
+
+# Giotto 4.0.4 (2024/02/28)
 
 ## Breaking changes
 * Remove `do_manual_adj` and image adjustment params from `createGiottoVisiumObject()`

R/general_help.R

@@ -1149,12 +1149,15 @@ readPolygonFilesVizgenHDF5 = function(boundaries_path,
 #' can be selected.
 #' @param file parquet file to load
 #' @param z_index either 'all' or a numeric vector of z_indices to get polygons for
+#' @param calc_centroids calculate centroids for the polygons (default = TRUE)
 #' @param verbose be verbose
-#' @keywords internal
 #' @export
-readPolygonVizgenParquet = function(file,
-                                    z_index = 'all',
-                                    verbose = TRUE) {
+readPolygonVizgenParquet = function(
+    file,
+    z_index = 'all',
+    calc_centroids = TRUE,
+    verbose = TRUE
+) {
 
   # package checks
   package_check('arrow')
@@ -1223,6 +1226,12 @@ readPolygonVizgenParquet = function(file,
       spatVector = sv,
       unique_ID_cache = poly_table$EntityID
     )
+
+    if(isTRUE(calc_centroids)) {
+      # NOTE: will not recalculate if centroids are already attached
+      gpoly = GiottoClass::centroids(x = gpoly, append_gpolygon = TRUE)
+    }
+
   })
 
   return(out)

R/spatial_genes.R

@@ -2026,10 +2026,11 @@ spatialDE <- function(gobject = NULL,
 
   # expression
   values = match.arg(expression_values, c('raw', 'normalized', 'scaled', 'custom'))
-  expr_values = get_expression_values(gobject = gobject,
-                                      spat_unit = spat_unit,
-                                      feat_type = feat_type,
-                                      values = values)
+  expr_values = getExpression(gobject = gobject,
+                              spat_unit = spat_unit,
+                              feat_type = feat_type,
+                              values = values,
+                              output = "matrix")
 
   ## python path
   if(is.null(python_path)) {
@@ -2042,9 +2043,10 @@ spatialDE <- function(gobject = NULL,
   reticulate::source_python(file = reader_path)
 
   ## get spatial locations
-  spatial_locs = get_spatial_locations(gobject,
-                                       spat_unit = spat_unit,
-                                       spat_loc_name = spat_loc_name)
+  spatial_locs = getSpatialLocations(gobject,
+                                     spat_unit = spat_unit,
+                                     name = spat_loc_name,
+                                     output = "data.table")
   spatial_locs <- as.data.frame(spatial_locs)
   rownames(spatial_locs) <- spatial_locs$cell_ID
   spatial_locs <- subset(spatial_locs, select = -cell_ID)
@@ -3810,6 +3812,9 @@ heatmSpatialCorFeats = function(gobject,
     stop('\n spatCorObject needs to be the output from detectSpatialCorFeats() \n')
   }
 
+  ## package check for ComplexHeatmap
+  package_check(pkg_name = 'ComplexHeatmap', repository = 'CRAN')
+
   ## create correlation matrix
   cor_DT = spatCorObject[['cor_DT']]
   cor_DT_dc = data.table::dcast.data.table(cor_DT, formula = feat_ID~variable, value.var = 'spat_cor')