0.4.12

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite Object Definitions and Framework
-Version: 0.4.10
+Version: 0.4.12
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -26,7 +26,7 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Depends:
-    R (>= 4.4.1)
+    R (>= 4.5.0)
 Imports:
     checkmate,
     data.table (>= 1.12.2),

NEWS.md

@@ -1,3 +1,14 @@
+# GiottoClass 0.4.12 (2025/12/12)
+
+## enhancements
+- automatic checking for `"count"` column in feature info
+
+## new
+- `misc` slot for storing unstructured data
+
+## enhancements
+- escape hatch for gobject initialize checking. Set option `"giotto.init_check_severity"` to `"stop"` (default), or `"warning"` depending on needs.
+
 # GiottoClass 0.4.10 (2025/09/30)
 
 ## bug fixes

R/aggregate.R

@@ -80,7 +80,9 @@ polygon_to_raster <- function(polygon, field = NULL) {
 #' in `feat_subset_column` in order to subset feature points when performing
 #' overlap calculation.
 #' @param count_info_column character. (optional) column with count information.
-#' Useful in cases when more than one detection is reported per point.
+#' Useful in cases when more than one detection is reported per point. If a
+#' column called "count" is present in the feature points data, it will be
+#' automatically selected.
 #' @param verbose be verbose
 #' @param \dots additional params to pass to methods.
 #' @details `feat_subset_column`, `feat_subset_ids`, and `count_info_column` are
@@ -328,6 +330,17 @@ setMethod(
     return_gpolygon = TRUE,
     verbose = TRUE,
     ...) {
+        if ("count" %in% names(y) && is.null(count_info_column)) {
+            vmsg(.v = verbose,
+                "[overlap] Found column \"count\" in feature info.
+                - Using as `count_info_column`
+                [!] Set count_info_column = FALSE to disable.")
+            count_info_column <- "count"
+        }
+        if (isFALSE(count_info_column)) {
+            count_info_column <- NULL
+        }
+
         res <- calculateOverlap(
             x = x[],
             y = y[],
@@ -1220,7 +1233,9 @@ calculateOverlapParallel <- function(gobject,
 #' @param x object containing overlaps info. Can be giotto object or SpatVector
 #' points or data.table of overlaps generated from `calculateOverlap`
 #' @param name name for the overlap count matrix
-#' @param count_info_column column with count information
+#' @param count_info_column column with count information. If a
+#' column called "count" is present in the feature points data, it will be
+#' automatically selected.
 #' @param \dots additional params to pass to methods
 #' @concept overlap
 #' @returns giotto object or count matrix
@@ -1260,7 +1275,7 @@ setMethod(
     ...) {
         type <- match.arg(type, choices = c("point", "intensity"))
         checkmate::assert_character(name, len = 1L)
-        if (!is.null(count_info_column)) {
+        if (!is.null(count_info_column) && !isFALSE(count_info_column)) {
             checkmate::assert_character(count_info_column, len = 1L)
         }
         checkmate::assert_logical(return_gobject)
@@ -1439,6 +1454,19 @@ setMethod(
 
 
         # 2. Perform aggregation to counts DT
+
+        # autodetect counts col
+        if ("count" %in% names(dtoverlap) && is.null(count_info_column)) {
+            vmsg(.v = verbose,
+                 "[overlap] Found column \"count\" in feature info.
+                - Using as `count_info_column`
+                [!] Set count_info_column = FALSE to disable.")
+            count_info_column <- "count"
+        }
+        if (isFALSE(count_info_column)) {
+            count_info_column <- NULL
+        }
+
         if (!is.null(count_info_column)) { # if there is a counts col
 
             if (!count_info_column %in% colnames(dtoverlap)) {

R/classes.R

@@ -453,13 +453,14 @@ updateGiottoObject <- function(gobject) {
     if (!is.null(attr(gobject, "OS_platform"))) {
         attr(gobject, "OS_platform") <- NULL
     }
-    if (is.null(attr(gobject, "versions"))) { # apply default version 0
+    if (is.null(attr(gobject, "versions"))) { # apply default version 0.0.0
         attr(gobject, "versions") <- .versions_info()
-        gobject@versions$gclass <- 0 # untracked
+        gobject@versions$gclass <- "0.0.0" # untracked
     }
 
     # warn if gobject newer than package
-    if (as.character(.gversion(gobject)) > as.character(packageVersion("GiottoClass"))) {
+    if (.gversion(gobject) >
+        numeric_version(packageVersion("GiottoClass"))) {
         warning(
             call. = FALSE,
             sprintf(
@@ -473,14 +474,19 @@ updateGiottoObject <- function(gobject) {
     # [version-based updates] -------------------------------------------------#
 
     # GiottoClass 0.3.0 removes @largeImages slot
-    if (.gversion(gobject) < "0.3.0") {
+    if (.gversion(gobject) < numeric_version("0.3.0")) {
         gobject <- .update_image_slot(gobject)
     }
 
     # GiottoClass 0.1.2 image updates moved here
     # TODO remove in future update
     gobject@images <- lapply(gobject@images, .update_giotto_image)
 
+    # GiottoClass 0.4.12 adds @misc slot
+    if (.gversion(gobject) < numeric_version("0.4.12")) {
+        attr(gobject, "misc") <- list()
+    }
+
     # -------------------------------------------------------------------------#
 
     # finally, set updated version number
@@ -567,6 +573,7 @@ updateGiottoObject <- function(gobject) {
 #' @slot join_info information about joined Giotto objects
 #' @slot multiomics multiomics integration results
 #' @slot h5_file path to h5 file
+#' @slot misc miscellaneous or unstructured data
 #' @details
 #'
 #' \[**initialize**\]
@@ -618,7 +625,8 @@ giotto <- setClass(
         versions = "list",
         join_info = "ANY",
         multiomics = "ANY",
-        h5_file = "ANY"
+        h5_file = "ANY",
+        misc = "list"
         # mirai = 'list'
     ),
     prototype = list(
@@ -643,7 +651,8 @@ giotto <- setClass(
         versions = .versions_info(),
         join_info = NULL,
         multiomics = NULL,
-        h5_file = NULL
+        h5_file = NULL,
+        misc = list()
         # mirai = list()
     )
 
@@ -694,7 +703,8 @@ setClass(
         versions = "ANY",
         join_info = "ANY",
         multiomics = "ANY",
-        h5_file = "ANY"
+        h5_file = "ANY",
+        misc = "list"
     ),
     prototype = list(
         packed_spatial_info = NULL,
@@ -718,7 +728,8 @@ setClass(
         versions = NULL,
         join_info = NULL,
         multiomics = NULL,
-        h5_file = NULL
+        h5_file = NULL,
+        misc = list()
     )
 )
 

R/combine_metadata.R

@@ -695,10 +695,10 @@ calculateLabelProportions <- function(gobject, labels,
         ), call. = FALSE)
     }
 
-    spat_unit = set_default_spat_unit(
+    spat_unit <- set_default_spat_unit(
         gobject = gobject, spat_unit = spat_unit
     )
-    feat_type = set_default_feat_type(
+    feat_type <- set_default_feat_type(
         gobject = gobject, spat_unit = spat_unit, feat_type = feat_type
     )
 
@@ -881,7 +881,7 @@ calculateLabelProportions <- function(gobject, labels,
         sn <- sn[, c("source", "target")] # drop weights info if any
     } else if (!"weight" %in% colnames(sn) || isFALSE(weights)) {
         warning(wrap_txt("No 'weight' information present in spatial network.
-                         Using adjacency instead."), call. = FALSE)
+                        Using adjacency instead."), call. = FALSE)
         sn[, "weight" := 1] # fallback if no weight info exists
     }
     # ensure unique

R/create.R

@@ -3136,7 +3136,7 @@ createGiottoImage <- function(gobject = NULL,
             if (transf == "flip_x_axis") {
                 mg_object <- magick::image_flop(mg_object)
             } else if (transf == "flip_y_axis") {
-                mg_object <- magick::image_flop(mg_object)
+                mg_object <- magick::image_flip(mg_object)
             } else {
                 wrap_msg(transf, " is not a supported transformation, see
                     details")

R/data_evaluation.R

@@ -152,7 +152,7 @@ evaluate_input <- function(type, x, ...) {
         .gstop(
             "expression input needs to be a path to matrix-like data or an",
             "object of class 'Matrix', 'data.table', 'data.frame', 'matrix'",
-      "'DelayedMatrix' or 'dbSparseMatrix'."
+            "'DelayedMatrix' or 'dbSparseMatrix'."
         )
     }
 
@@ -321,7 +321,7 @@ evaluate_input <- function(type, x, ...) {
     rnames <- rownames(x)
     if (!is.null(rnames)) {
         vmsg(.v = verbose, "[spatlocs] matrix input has rownames.
-             Using these as IDs.")
+            Using these as IDs.")
         dt[, id := rnames]
     }
     .evaluate_spatial_locations(dt, verbose = verbose, ...)

R/images.R

@@ -2850,7 +2850,7 @@ to_simple_tif <- function(input_file,
             unlink(outpath, force = TRUE) # if overwrite, delete original
         } else {
             stop("File already exists: ", outpath,
-                 "\nSet overwrite = TRUE to replace.\n",
+                "\nSet overwrite = TRUE to replace.\n",
                 call. = FALSE
             )
         }
@@ -2884,11 +2884,11 @@ ometif_to_tif <- to_simple_tif
 #' "integer"). `output = "structure"` can help
 #' with figuring out which is most appropriate.
 #' @param output character. One of "data.frame" to return a data.frame of the
-#' attributes information of the xml node, "xmL" for an \{xml2\} representation
+#' attributes information of the xml node, "xml" for an \{xml2\} representation
 #' of the node, "list" for an R native list (note that many items in the
-#' list may have overlapping names that make indexing difficult), or
+#' list may have overlapping names that make indexing difficult),
 #' "structure" to invisibly return NULL, but print the structure of the XML
-#' document or node.
+#' document/node, or "kv" (extract key/value pairs from OME MapAnnotations).
 #' @returns list/data.frame/XML depending on `output`
 #' @examples
 #' if (FALSE) {
@@ -2911,7 +2911,7 @@ tif_metadata <- function(path,
     node = NULL,
     page = NULL,
     type = c("attribute", "text", "double", "integer"),
-    output = c("data.frame", "xml", "list", "structure")) {
+    output = c("data.frame", "xml", "list", "structure", "kv")) {
     checkmate::assert_file_exists(path)
     package_check(
         pkg_name   = c("tifffile", "imagecodecs", "xml2"),
@@ -2923,7 +2923,7 @@ tif_metadata <- function(path,
     img <- TIF$TiffFile(path)
     on.exit(try(img$close(), silent = TRUE), add = TRUE)
     output <- match.arg(output,
-        choices = c("data.frame", "xml", "list", "structure")
+        choices = c("data.frame", "xml", "list", "structure", "kv")
     )
     type <- match.arg(type,
         choices = c("attribute", "text", "double", "integer")
@@ -2992,12 +2992,14 @@ ometif_metadata <- tif_metadata
         # qptiff: per-page description
         p1 <- as.integer(page)[1]
         x  <- tryCatch(img$pages[[p1 - 1L]]$description, error = function(e) NULL)
+        if (is.null(x) || !nzchar(x)) {
+            x <- tryCatch(img$series[[1]]$pages[[p1 - 1L]]$description, error = function(e) NULL)
+        }
     } else if (img$is_fluoview) x <- img$fluoview_metadata
     else if (img$is_nih) x <- img$nih_metadata
     else if (img$is_astrotiff) x <- img$astrotiff_metadata
     else if (img$is_imagej) x <- img$imagej_metadata
     else if (img$is_lsm) x <- img$lsm_metadata
-    else if (img$is_qpi) x <- img$series[[1]]$pages[[page - 1L]]$description
     else if (img$is_micromanager) x <- img$micromanager_metadata
     else stop("unrecognized tif format\n", call. = FALSE)
 
@@ -3009,6 +3011,20 @@ ometif_metadata <- tif_metadata
     ns <- xml2::xml_ns(x)
     has_namespace <- length(ns) > 0L
 
+    ## NEW: output = "kv" (read OME MapAnnotation K/Vs) ---
+    if (identical(output, "kv")) {
+        m_nodes <- xml2::xml_find_all(
+            x,
+            ".//*[local-name()='StructuredAnnotations']//*[local-name()='MapAnnotation']/*[local-name()='Value']//*[local-name()='M']"
+        )
+        if (!length(m_nodes)) return(NULL)
+        keys   <- xml2::xml_attr(m_nodes, "K")
+        values <- xml2::xml_text(m_nodes)
+        out <- as.list(values)
+        names(out) <- keys
+        return(out)
+    }
+
     if (!is.null(node)) {
         node_parts <- node
         node_path  <- paste(node_parts, collapse = "/")