Merge pull request #73 from drieslab/dev

v0.0.0.9008

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.0.0.9007
+Version: 0.0.0.9008
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),

NAMESPACE

@@ -16,6 +16,7 @@ export(addGiottoPolygons)
 export(addNetworkLayout)
 export(addSpatialCentroidLocations)
 export(addSpatialCentroidLocationsLayer)
+export(add_img_array_alpha)
 export(aggregateStacks)
 export(aggregateStacksExpression)
 export(aggregateStacksLocations)
@@ -26,13 +27,16 @@ export(anndataToGiotto)
 export(annotateGiotto)
 export(annotateSpatialGrid)
 export(annotateSpatialNetwork)
+export(annotate_spatlocs_with_spatgrid_2D)
+export(annotate_spatlocs_with_spatgrid_3D)
 export(calculateMetaTable)
 export(calculateMetaTableCells)
 export(calculateOverlapParallel)
 export(calculateOverlapPolygonImages)
 export(calculateOverlapRaster)
 export(calculateOverlapSerial)
 export(calculateSpatCellMetadataProportions)
+export(calculate_overlap_raster)
 export(changeGiottoInstructions)
 export(changeImageBg)
 export(checkGiottoEnvironment)
@@ -116,6 +120,7 @@ export(get_adj_rescale_img)
 export(get_args)
 export(get_cell_metadata)
 export(get_dimReduction)
+export(get_distance)
 export(get_expression_values)
 export(get_feature_info)
 export(get_feature_metadata)
@@ -310,6 +315,7 @@ exportMethods("spatUnit<-")
 exportMethods(activeFeatType)
 exportMethods(activeSpatUnit)
 exportMethods(as.sf)
+exportMethods(as.stars)
 exportMethods(centroids)
 exportMethods(colnames)
 exportMethods(copy)

NEWS.md

@@ -8,8 +8,9 @@
 - Added `crop()` method for `giottoLargeImage`, `giottoPoints`
 - Added `terraVectData` as virtual parent class for `giottoPolygon` and `giottoPoints` classes
 - Added `$` and `$<-` methods for `terraVectData`
-- Added `[` subsetting for `giottoPoints` and `giottoPolygon`
+- Added `[` subsetting for `giottoPoints` and `giottoPolygon` with numerical, logical, and character (by ID)
 - Added `setGiotto()` generic
+- Added `as.sf()` and `as.stars()` converters for `giottoPoints` and `giottoPolygon` 
 
 ## Changes
 - Improved performance of gefToGiotto()

R/aggregate.R

@@ -52,12 +52,13 @@ polygon_to_raster = function(polygon, field = NULL) {
 
 #' @title calculateOverlapRaster
 #' @name calculateOverlapRaster
-#' @description calculate overlap between cellular structures (polygons) and features (points)
+#' @description calculate overlap between cellular structures (polygons) and
+#' features (points).
 #' @param gobject giotto object
 #' @param name_overlap name for the overlap results (default to feat_info parameter)
-#' @param spatial_info polygon information
+#' @param spatial_info character. name polygon information
 #' @param poly_ID_names (optional) list of poly_IDs to use
-#' @param feat_info feature information
+#' @param feat_info character. name of feature information
 #' @param feat_subset_column feature info column to subset features with
 #' @param feat_subset_ids ids within feature info column to use for subsetting
 #' @param count_info_column column with count information (optional)
@@ -66,26 +67,20 @@ polygon_to_raster = function(polygon, field = NULL) {
 #' @return giotto object or spatVector with overlapping information
 #' @details Serial overlapping function.
 #' @concept overlap
+#' @seealso [calculate_overlap_raster()]
 #' @export
-calculateOverlapRaster = function(gobject,
-                                  name_overlap = NULL,
-                                  spatial_info = NULL,
-                                  poly_ID_names = NULL,
-                                  feat_info = NULL,
-                                  feat_subset_column = NULL,
-                                  feat_subset_ids = NULL,
-                                  count_info_column = NULL,
-                                  return_gobject = TRUE,
-                                  verbose = TRUE) {
-
-  # define for :=
-  poly_ID = NULL
-  poly_i = NULL
-  ID = NULL
-  x = NULL
-  y = NULL
-  feat_ID = NULL
-  feat_ID_uniq = NULL
+calculateOverlapRaster = function(
+    gobject,
+    name_overlap = NULL,
+    spatial_info = NULL,
+    poly_ID_names = NULL,
+    feat_info = NULL,
+    feat_subset_column = NULL,
+    feat_subset_ids = NULL,
+    count_info_column = NULL,
+    return_gobject = TRUE,
+    verbose = TRUE
+) {
 
   # set defaults if not provided
   if(is.null(feat_info)) {
@@ -101,30 +96,84 @@ calculateOverlapRaster = function(gobject,
   }
 
 
-  # spatial vector
-  if(verbose) cat('1. convert polygon to raster \n')
-  spatvec = gobject@spatial_info[[spatial_info]]@spatVector
+  # get information from gobject
+  # * spatial vector
+  spatvec = getPolygonInfo(
+    gobject = gobject,
+    polygon_name = spatial_info,
+    return_giottoPolygon = FALSE
+  )
+
+  # * point vector
+  pointvec = getFeatureInfo(
+    gobject = gobject,
+    feat_type = feat_info,
+    return_giottoPoints = FALSE,
+    set_defaults = FALSE
+  )
+
 
-  # subset spatvec
+  # subset points and polys if needed
+  # * subset spatvec
   if(!is.null(poly_ID_names)) {
     spatvec = spatvec[spatvec$poly_ID %in% poly_ID_names]
   }
 
-  # spatial vector to raster
-  spatrast_res = polygon_to_raster(spatvec, field = 'poly_ID')
-  spatrast = spatrast_res[['raster']]
-  ID_vector = spatrast_res[['ID_vector']]
-
-  # point vector
-  pointvec = gobject@feat_info[[feat_info]]@spatVector
-
-  # subset points if needed
+  # * subset points if needed
   # e.g. to select transcripts within a z-plane
   if(!is.null(feat_subset_column) & !is.null(feat_subset_ids)) {
     bool_vector = pointvec[[feat_subset_column]][[1]] %in% feat_subset_ids
     pointvec = pointvec[bool_vector]
   }
 
+  # run overlap workflow
+  overlap_points = calculate_overlap_raster(
+    spatvec = spatvec,
+    pointvec = pointvec,
+    count_info_column = count_info_column,
+    verbose = verbose
+  )
+
+  # return values
+  if(isTRUE(return_gobject)) {
+
+    if(is.null(name_overlap)) name_overlap = feat_info
+    gobject@spatial_info[[spatial_info]]@overlaps[[name_overlap]] = overlap_points
+    return(gobject)
+
+  } else {
+    return(overlap_points)
+  }
+}
+
+
+
+#' @name calculate_overlap_raster
+#' @title Find feature points overlapped by rasterized polygon.
+#' @description Core workflow function that accepts simple `SpatVector` inputs,
+#' performs rasterization of the polys and then checks for overlaps.
+#' @param spatvec `SpatVector` polygon from a `giottoPolygon` object
+#' @param pointvec `SpatVector` points from a `giottoPoints` object
+#' @param count_info_column column with count information (optional)
+#' @param verbose be verbose
+#' @return `SpatVector` of overlapped points info
+#' @concept overlap
+#' @seealso [calculateOverlapRaster()]
+#' @export
+calculate_overlap_raster = function(spatvec,
+                                    pointvec,
+                                    count_info_column = NULL,
+                                    verbose = TRUE) {
+
+  # DT vars
+  poly_ID = poly_i = ID = x = y = feat_ID = feat_ID_uniq = NULL
+
+  # spatial vector to raster
+  if(verbose) cat('1. convert polygon to raster \n')
+  spatrast_res = polygon_to_raster(spatvec, field = 'poly_ID')
+  spatrast = spatrast_res[['raster']]
+  ID_vector = spatrast_res[['ID_vector']]
+
   ## overlap between raster and point
   if(verbose) cat('2. overlap raster and points \n')
   overlap_test = terra::extract(x = spatrast, y = pointvec)
@@ -136,7 +185,7 @@ calculateOverlapRaster = function(gobject,
 
   # add point information
   if(verbose) cat('4. add points information \n')
-  pointvec_dt = spatVector_to_dt(pointvec)
+  pointvec_dt = data.table::as.data.table(pointvec, geom = "XY")
 
   pointvec_dt_x = pointvec_dt$x ; names(pointvec_dt_x) = pointvec_dt$geom
   pointvec_dt_y = pointvec_dt$y ; names(pointvec_dt_y) = pointvec_dt$geom
@@ -154,25 +203,15 @@ calculateOverlapRaster = function(gobject,
   }
 
   if(verbose) cat('5. create overlap polygon information \n')
-  overlap_test_dt_spatvector = terra::vect(x = as.matrix(overlap_test_dt[, c('x', 'y'), with = F]),
-                                           type = "points",
-                                           atts = overlap_test_dt[, c('poly_ID', 'feat_ID', 'feat_ID_uniq', count_info_column), with = F])
-  names(overlap_test_dt_spatvector) = c('poly_ID', 'feat_ID', 'feat_ID_uniq', count_info_column)
-
-
-
-  if(return_gobject == TRUE) {
-    if(is.null(name_overlap)) {
-      name_overlap = feat_info
-    }
-
-    gobject@spatial_info[[spatial_info]]@overlaps[[name_overlap]] = overlap_test_dt_spatvector
-    return(gobject)
-
-  } else {
-    return(overlap_test_dt_spatvector)
-  }
-
+  overlap_test_dt_spatvector = terra::vect(
+    x = as.matrix(overlap_test_dt[, c('x', 'y'), with = F]),
+    type = "points",
+    atts = overlap_test_dt[, c('poly_ID', 'feat_ID', 'feat_ID_uniq', count_info_column), with = F]
+  )
+  names(overlap_test_dt_spatvector) = c(
+    'poly_ID', 'feat_ID', 'feat_ID_uniq', count_info_column
+  )
+  return(overlap_test_dt_spatvector)
 }
 
 

R/classes.R

@@ -475,7 +475,8 @@ updateGiottoObject <- function(gobject) {
 #' that are provided in the expression slot.
 #'
 #'
-#' @export
+#' @export giotto
+#' @exportClass giotto
 giotto <- setClass(
   "giotto",
   slots = c(
@@ -658,8 +659,8 @@ check_expr_obj <- function(object) {
 #' @slot feat_type feature type of expression (e.g. 'rna', 'protein')
 #' @slot provenance origin data of expression information (if applicable)
 #' @slot misc misc
-#' @export
-setClass("exprObj",
+#' @exportClass exprObj
+exprObj = setClass("exprObj",
   contains = c("nameData", "exprData", "spatFeatData", "miscData", 'giottoSubobject'),
   validity = check_expr_obj
 )
@@ -713,8 +714,8 @@ check_cell_meta_obj <- function(object) {
 #' @slot spat_unit spatial unit of aggregated expression (e.g. 'cell')
 #' @slot feat_type feature type of aggregated expression (e.g. 'rna', 'protein')
 #' @slot provenance origin data of aggregated expression information (if applicable)
-#' @export
-setClass("cellMetaObj",
+#' @exportClass cellMetaObj
+cellMetaObj = setClass("cellMetaObj",
   contains = c("metaData", "spatFeatData", "giottoSubobject"),
   validity = check_cell_meta_obj
 )
@@ -758,8 +759,8 @@ check_feat_meta_obj <- function(object) {
 #' @slot spat_unit spatial unit of aggregated expression (e.g. 'cell')
 #' @slot feat_type feature type of aggregated expression (e.g. 'rna', 'protein')
 #' @slot provenance origin data of aggregated expression information (if applicable)
-#' @export
-setClass("featMetaObj",
+#' @exportClass featMetaObj
+featMetaObj = setClass("featMetaObj",
   contains = c("metaData", "spatFeatData", 'giottoSubobject'),
   validity = check_feat_meta_obj
 )
@@ -825,8 +826,8 @@ check_dim_obj <- function(object) {
 #' @slot reduction_method method used to generate dimension reduction
 #' @slot coordinates embedding coordinates
 #' @slot misc method-specific additional outputs
-#' @export
-setClass("dimObj",
+#' @exportClass dimObj
+dimObj = setClass("dimObj",
   contains = c("nameData", "spatFeatData", 'giottoSubobject'),
   slots = c(
     reduction = "character",
@@ -888,8 +889,8 @@ S3toS4dimObj <- function(object) {
 #' @slot spat_unit spatial unit of data
 #' @slot provenance origin of aggregated information (if applicable)
 #' @slot misc misc
-#' @export
-setClass("nnNetObj",
+#' @exportClass nnNetObj
+nnNetObj = setClass("nnNetObj",
   contains = c("nameData", "nnData", "spatFeatData", "miscData", 'giottoSubobject')
 )
 
@@ -955,8 +956,8 @@ check_spat_locs_obj <- function(object) {
 #' @slot coordinates data.table of spatial coordinates/locations
 #' @slot spat_unit spatial unit tag
 #' @slot provenance origin of aggregated information (if applicable)
-#' @export
-setClass("spatLocsObj",
+#' @exportClass spatLocsObj
+spatLocsObj =  setClass("spatLocsObj",
   contains = c("nameData", "coordDataDT", "spatData", "miscData", 'giottoSubobject'),
   validity = check_spat_locs_obj
 )
@@ -1467,7 +1468,8 @@ giottoImage <- setClass(
 #' @slot is_int values are integers
 #' @slot file_path file path to the image if given
 #' @slot OS_platform Operating System to run Giotto analysis on
-#' @export
+#' @export giottoLargeImage
+#' @exportClass giottoLargeImage
 giottoLargeImage <- setClass(
   Class = "giottoLargeImage",
   slots = c(

R/create.R

@@ -659,12 +659,6 @@ createGiottoObjectSubcellular = function(gpolygons = NULL,
       centroidsDT_loc = centroidsDT[, .(poly_ID, x, y)]
       colnames(centroidsDT_loc) = c('cell_ID', 'sdimx', 'sdimy')
 
-      # gobject = set_spatial_locations(gobject = gobject,
-      #                                 spat_unit = polygon_info,
-      #                                 spat_loc_name = 'raw',
-      #                                 spatlocs = centroidsDT_loc,
-      #                                 verbose = FALSE)
-
       locsObj = create_spat_locs_obj(name = 'raw',
                                      coordinates = centroidsDT_loc,
                                      spat_unit = polygon_info,
@@ -778,9 +772,7 @@ createGiottoObjectSubcellular = function(gpolygons = NULL,
         gobject@feat_metadata[[feat_type]] = data.table::as.data.table(gobject@feat_metadata[[feat_type]])
         gobject@feat_metadata[[feat_type]][, feat_ID := gobject@feat_ID[[feat_type]]]
       }
-
     }
-
   }
 
 

R/generate_poly.R

@@ -41,7 +41,7 @@ polyStamp <- function(stamp_dt,
   centroid_dt = data.table::as.data.table(terra::centroids(stamp_poly),
                               geom = "XY",
                               include_values = F)
-  
+
   stamp_centroid = c(x = centroid_dt$x,
                      y = centroid_dt$y)
 
@@ -279,3 +279,9 @@ makePseudoVisium <- function(extent = NULL,
                               skip_eval_dfr = TRUE,
                               copy_dt = FALSE)
 }
+
+
+
+
+
+

R/generics.R

@@ -69,4 +69,5 @@ setGeneric('setGiotto', function(gobject, x, ...) standardGeneric('setGiotto'))
 
 # coerce ####
 setGeneric('as.sf', function(x, ...) standardGeneric('as.sf'))
+setGeneric('as.stars', function(x, ...) standardGeneric('as.stars'))