chore: catch up to dev

DESCRIPTION

@@ -105,6 +105,7 @@ Collate:
     'interoperability.R'
     'join.R'
     'methods-IDs.R'
+    'methods-XY.R'
     'methods-affine.R'
     'methods-centroids.R'
     'methods-coerce.R'

NAMESPACE

@@ -298,6 +298,7 @@ exportMethods("$")
 exportMethods("$<-")
 exportMethods("+")
 exportMethods("-")
+exportMethods("XY<-")
 exportMethods("[")
 exportMethods("[<-")
 exportMethods("[[")
@@ -309,6 +310,7 @@ exportMethods("instructions<-")
 exportMethods("objName<-")
 exportMethods("prov<-")
 exportMethods("spatUnit<-")
+exportMethods(XY)
 exportMethods(activeFeatType)
 exportMethods(activeSpatUnit)
 exportMethods(affine)

NEWS.md

@@ -9,6 +9,8 @@
 - fix `joinGiottoObject()` for gobjects with only poly and point data [#233](https://github.com/drieslab/GiottoClass/issues/233)
 - fix `joinGiottoObject()` for gobjects with image intensity overlaps features
 - fix subsetting error due to expression `matrix` drop to `numeric` when only one cell is left
+- `shift_vertical_step` and `shift_horizontal_step` args in `createGiottoPolygonsFromMask()` when numeric now shift by steps based on the dims of the image instead of just by the numerical value provided.
+- fix feature metadata not being mixedsorted after join
 
 ## enhancements
 - python packages to install through pip is now settable in `installGiottoEnvironment()` [#224](https://github.com/drieslab/GiottoClass/issues/224)
@@ -22,11 +24,14 @@
 - `ext()` and `ext<-()` can now be used to get and set extent of `affine2d`
 - `rownames()`, `colnames()`, `dimnames()` for `giotto`
 - `spatValues()` can get values from multiple spatial units.
+- `createGiottoPolygonsFromMask()` now works with anything `terra::rast()` can read
+- `createGiottoLargeImage()` now works with anything `terra::rast()` can read
 
 ## new
 - `sliceGiotto()` for pulling out specific spatial units and feature types as independent `giotto` objects
 - `splitGiotto()` for splitting a Giotto object into a list of Giotto objects based on a cell metadata column
 - `as.list()` method for `giotto` to dump the data as a list of subobjects
+- `XY()` and `XY<-()` for accessing and setting coordinate values of subobjects as `matrix`
 
 
 # GiottoClass 0.3.5 (2024/08/28)

R/create.R

@@ -2418,7 +2418,8 @@ setMethod(
 
 
 #' @rdname createGiottoPolygon
-#' @param maskfile path to mask file
+#' @param maskfile path to mask file, a terra `SpatRaster`, or some other
+#' data class readable by [terra::rast()]
 #' @param mask_method how the mask file defines individual segmentation
 #' annotations. See *mask_method* section
 #' @param name character. Name to assign created `giottoPolygon`
@@ -2521,15 +2522,16 @@ createGiottoPolygonsFromMask <- function(maskfile,
 
     # if maskfile input is not a spatraster, read it in as spatraster
     # if it is spatraster, skip
-    if (!inherits(maskfile, "SpatRaster")) {
+    if (inherits(maskfile, "SpatRaster")) {
+        terra_rast <- maskfile
+    } else if (is.character(maskfile)) {
         # check if mask file exists
         maskfile <- path.expand(maskfile)
-        if (!file.exists(maskfile)) {
-            stop("path : ", maskfile, " does not exist \n")
-        }
+        checkmate::assert_file_exists(maskfile)
         terra_rast <- .create_terra_spatraster(maskfile)
     } else {
-        terra_rast <- maskfile
+        # assume some other class readable by terra::rast()
+        terra_rast <- .create_terra_spatraster(maskfile)
     }
 
     # create polygons from mask
@@ -2627,14 +2629,14 @@ createGiottoPolygonsFromMask <- function(maskfile,
     if (identical(shift_vertical_step, TRUE)) {
         shift_vertical_step <- rast_dimensions[1] # nrows of raster
     } else if (is.numeric(shift_vertical_step)) {
-        shift_vertical_step <- shift_vertical_step
+        shift_vertical_step <- rast_dimensions[1] * shift_vertical_step
     } else {
         shift_vertical_step <- 0
     }
     if (identical(shift_horizontal_step, TRUE)) {
         shift_horizontal_step <- rast_dimensions[2] # ncols of raster
     } else if (is.numeric(shift_horizontal_step)) {
-        shift_horizontal_step <- shift_horizontal_step
+        shift_horizontal_step <- rast_dimensions[2] * shift_horizontal_step
     } else {
         shift_horizontal_step <- 0
     }
@@ -3174,7 +3176,8 @@ createGiottoImage <- function(
 #' @name createGiottoLargeImage
 #' @description Creates a large giotto image that can be added to a Giotto
 #' subcellular object. Generates deep copy of SpatRaster
-#' @param raster_object terra SpatRaster image object
+#' @param raster_object filepath to an image, a terra `SpatRaster` or, other format
+#' openable via [terra::rast()]
 #' @param name name for the image
 #' @param negative_y Map image to negative y spatial values if TRUE. Meaning
 #' that origin is in upper left instead of lower left.
@@ -3216,42 +3219,25 @@ createGiottoLargeImage <- function(
     # create minimum giotto
     g_imageL <- new("giottoLargeImage", name = name)
 
-
     ## 1. check raster object and load as SpatRaster if necessary
-    if (!inherits(raster_object, "SpatRaster")) {
-        if (file.exists(raster_object)) {
-            g_imageL@file_path <- raster_object
-            raster_object <- .create_terra_spatraster(
-                image_path = raster_object
-            )
-        } else {
-            stop("raster_object needs to be a 'SpatRaster' object from the
-                terra package or \n an existing path that can be read by
-                terra::rast()")
-        }
-    }
-
-    # Prevent updates to original raster object input
-    if (getNamespaceVersion("terra") >= "1.15-12") {
+    if (inherits(raster_object, "SpatRaster")) {
+        # Prevent updates to original raster object input
         raster_object <- terra::deepcopy(raster_object)
+    } else if (is.character(raster_object)) {
+        checkmate::assert_file_exists(raster_object)
+        g_imageL@file_path <- raster_object
+        raster_object <- .create_terra_spatraster(raster_object)
     } else {
-        # raster_object = terra::copy(raster_object)
-        if (isTRUE(verbose)) {
-            warning("\n If largeImage was created from a terra raster object,
-                    manipulations to the giotto image may be reflected in the
-                    raster object as well. Update terra to >= 1.15-12 to avoid
-                    this issue. \n")
-        }
+        # assume class readable by terra rast
+        raster_object <- .create_terra_spatraster(raster_object)
     }
 
 
     ## 2. image bound spatial extent
-    if (use_rast_ext == TRUE) {
+    if (use_rast_ext) {
         extent <- terra::ext(raster_object)
-        if (verbose == TRUE) {
-            wrap_msg("use_rast_ext == TRUE, extent from input raster_object will
-                be used.")
-        }
+        vmsg(.v = verbose, "use_rast_ext == TRUE
+        extent from input raster_object will be used.")
     }
 
     # By extent object (priority)

R/generics.R

@@ -33,14 +33,6 @@ setGeneric(
 )
 
 
-# Methods and documentations found in methods-spatShift.R
-setGeneric("spatShift", function(x, ...) standardGeneric("spatShift"))
-setGeneric("affine", function(x, y, ...) standardGeneric("affine"))
-setGeneric("shear", function(x, ...) standardGeneric("shear"))
-
-# Methods and documentations found in methods-overlaps.R
-setGeneric("overlaps", function(x, ...) standardGeneric("overlaps"))
-
 
 # Object creation ####
 setGeneric(
@@ -119,6 +111,17 @@ setGeneric("norm_pearson", function(x, ...) standardGeneric("norm_pearson"))
 setGeneric("norm_osmfish", function(x, ...) standardGeneric("norm_osmfish"))
 
 
+# Methods and documentations found in methods-spatShift.R
+setGeneric("spatShift", function(x, ...) standardGeneric("spatShift"))
+setGeneric("affine", function(x, y, ...) standardGeneric("affine"))
+setGeneric("shear", function(x, ...) standardGeneric("shear"))
+setGeneric("XY", function(x, ...) standardGeneric("XY"))
+setGeneric("XY<-", function(x, ..., value) standardGeneric("XY<-"))
+
+# Methods and documentations found in methods-overlaps.R
+setGeneric("overlaps", function(x, ...) standardGeneric("overlaps"))
+
+
 
 # Giotto subnesting ####
 # All methods and documentations found in methods-nesting.R

R/join.R

@@ -4,19 +4,17 @@
 #' @name .join_expression_matrices
 #' @keywords internal
 #' @noRd
-.join_expression_matrices <- function(matrix_list) {
+.join_expression_matrices <- function(matrix_list, feat_ids = NULL) {
+
     # find all features
-    final_feats <- list()
-    for (matr_i in seq_len(length(matrix_list))) {
-        rowfeats <- rownames(matrix_list[[matr_i]])
-        final_feats[[matr_i]] <- rowfeats
+    if (is.null(feat_ids)) {
+        final_feats <- lapply(matrix_list, rownames)
+        final_feats <- unique(unlist(final_feats))
+    } else {
+        final_feats <- feat_ids
     }
-
-    final_feats <- unique(unlist(final_feats))
     final_feats <- mixedsort(final_feats)
 
-
-
     # extend matrices with missing ids
     final_mats <- list()
     for (matr_i in seq_len(length(matrix_list))) {
@@ -60,9 +58,20 @@
 #' @name .join_feat_meta
 #' @keywords internal
 #' @noRd
-.join_feat_meta <- function(dt_list) {
+.join_feat_meta <- function(dt_list, feat_ids = NULL) {
     feat_ID <- NULL
 
+    if (!is.null(feat_ids)) {
+        dt_list <- lapply(dt_list, function(dt) {
+            dt <- dt[feat_ID %in% feat_ids]
+            missing_feat <- dt[, feat_ids[!feat_ids %in% feat_ID]]
+            if (length(missing_feat) > 0L) {
+                dt_append <- data.table::data.table(feat_ID = missing_feat)
+                dt <- rbind(dt, dt_append, fill = TRUE)
+            }
+        })
+    }
+
     comb_meta <- do.call("rbind", c(dt_list, fill = TRUE))
     comb_meta <- unique(comb_meta)
 
@@ -77,8 +86,12 @@
             "feature metadata: multiple versions of metadata for:\n",
             dup_feats,
             "\n First entry will be selected for joined object."
+            # "first" is based on gobject order
         ))
     }
+
+    # order by feat_ID
+    comb_meta <- comb_meta[mixedorder(feat_ID)]
 
     return(comb_meta)
 }