Merge pull request #221 from drieslab/dev2

v0.3.5

.github/workflows/dev_check.yml

@@ -84,16 +84,24 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Test python env install
+      - name: setup giotto_env
+        shell: Rscript {0}
         run: |
-          if (!GiottoClass::checkGiottoEnvironment()) {
+          if (!GiottoClass::checkGiottoEnvironment(envname = "giotto_env")) {
             GiottoClass::installGiottoEnvironment()
           }
 
-          reticulate::py_list_packages(envname = "giotto_env")
-          reticulate::conda_install(envname = 'giotto_env',packages = 'scanpy',pip = TRUE)
-        shell: Rscript {0}
-
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
+        
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2
         with:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.3.4
+Version: 0.3.5
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),

NAMESPACE

@@ -9,6 +9,7 @@ S3method(.DollarNames,terraVectData)
 S3method(as.data.table,SpatVector)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
+S3method(print,giottoInstructions)
 S3method(t,spatLocsObj)
 S3method(t,spatialNetworkObj)
 export(addCellMetadata)
@@ -324,6 +325,7 @@ exportMethods("spatUnit<-")
 exportMethods(activeFeatType)
 exportMethods(activeSpatUnit)
 exportMethods(affine)
+exportMethods(as.character)
 exportMethods(as.matrix)
 exportMethods(as.points)
 exportMethods(as.polygons)
@@ -408,8 +410,10 @@ importMethodsFrom(terra,as.points)
 importMethodsFrom(terra,as.polygons)
 importMethodsFrom(terra,centroids)
 importMethodsFrom(terra,crop)
+importMethodsFrom(terra,density)
 importMethodsFrom(terra,ext)
 importMethodsFrom(terra,flip)
+importMethodsFrom(terra,hist)
 importMethodsFrom(terra,ncol)
 importMethodsFrom(terra,nrow)
 importMethodsFrom(terra,plot)

NEWS.md

@@ -1,4 +1,25 @@
 
+# GiottoClass 0.3.5 (2024/08/28)
+
+## breaking changes
+- `set_giotto_python_path()` will now also initialize python env to set by default and print which python env is active, but otherwise do nothing if any python env has already been initialized.
+- deprecated `readGiottoInstructions()`, `showGiottoInstructions()`, `changeGiottoInstructions()`, `replaceGiottoInstructions()` in favor of `instructions()` generic
+
+## bug fixes
+- intensity images now automatically scale to estimated highest value
+- `giottoPolygon` `plot()` default `max_poly` raised to `1e6`
+- `giottoInstructions` no longer lose class when specific params are replaced
+- `ometif_to_tif()` now checks for _imagecodecs_ package as well
+- `anndataToGiotto()` and `giottoToAnndata` now check for _anndata_ package as well.
+- fix `joinGiottoObjects()` `"z_stack"` join method
+- fix error in documentation [#214](https://github.com/drieslab/GiottoClass/issues/214) by shaojunyu
+- fix error in `installGiottoEnvironment()` [#1006](https://github.com/drieslab/Giotto/issues/1006) by 13954380607
+
+## enhancements
+- `print()` method for `giottoInstructions`
+- `rbind()` for `spatLocsObj`
+
+
 # GiottoClass 0.3.4 (2024/08/04)
 
 ## bug fixes

R/globals.R

@@ -4,7 +4,9 @@ utils::globalVariables(
         "python_leiden", "python_louvain", "python_spatial_genes",
         "Spatial_DE_AEH", "Spatial_DE", "silhouette_rank",
         "python_scrublet", "python_create_mesmer_app",
-        "python_segment_image", "ad_guard", "dir_guard", "ad_obj",
+        "python_segment_image", 
+        # anndata interop
+        "ad_guard", "dir_guard", "ad_obj",
         "lay_inv", "set_adg_layer_data", "set_adg_spat_locs",
         "set_adg_metadata", "set_adg_pca", "set_adg_umap",
         "set_adg_tsne", "write_ad_h5ad", "read_anndata_from_path",
@@ -15,6 +17,11 @@ utils::globalVariables(
         "extract_layered_data", "set_adg_nn", "find_NN_keys",
         "extract_NN_connectivities", "extract_NN_distances",
         "extract_NN_info", "align_network_data", "extract_SN_connectivities",
-        "extract_SN_distances", "set_adg_sn", "create_AnnData", "ometif_2_tif"
+        "extract_SN_distances", "set_adg_sn", "create_AnnData", 
+        # tifffile
+        "ometif_2_tif",
+        # spatialdata interop
+        "createSpatialData", "read_spatialdata_from_path", "extract_spatial",
+        "extract_image"
     )
 )

R/images.R

@@ -2644,23 +2644,31 @@ distGiottoImage <- function(
 #' gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE)
 #'
 #' density(gimg)
+NULL
+
+#' @rdname density
 #' @export
 setMethod(
     "density", signature("giottoLargeImage"),
     function(x, show_max = TRUE, ...) {
-        a <- list(x = x@raster_object, ...)
-        res <- do.call(terra::density, args = a)
-
-        if (isFALSE(a$plot)) {
-            return(res)
-        }
-
-        if (isTRUE(show_max)) {
-            graphics::abline(v = x@max_window, col = "red")
-        }
+        a <- get_args_list(...)
+        do.call(.density_giottolargeimage, args = a)
     }
 )
 
+.density_giottolargeimage <- function(x, show_max = TRUE, ...) {
+    a <- list(x = x@raster_object, ...)
+    res <- do.call(terra::density, args = a)
+
+    if (isFALSE(a$plot)) {
+        return(res)
+    }
+
+    if (isTRUE(show_max)) {
+        graphics::abline(v = x@max_window, col = "red")
+    }
+}
+
 
 #' @name hist
 #' @title Histogram
@@ -2677,6 +2685,9 @@ setMethod(
 #' gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE, verbose = FALSE)
 #'
 #' hist(gimg)
+NULL
+
+#' @rdname hist
 #' @export
 setMethod(
     "hist", signature("giottoLargeImage"),
@@ -2745,7 +2756,11 @@ ometif_to_tif <- function(input_file,
     a <- list(input_file = input_file)
 
     # get tifffile py
-    package_check("tifffile", repository = "pip:tifffile")
+    package_check(
+        pkg_name = c("tifffile", "imagecodecs"), 
+        repository = c("pip:tifffile", "pip:imagecodecs")
+    )
+
     ometif2tif_path <- system.file(
         "python", "ometif_convert.py",
         package = "GiottoClass"

R/instructions.R

@@ -1,9 +1,7 @@
 # Giotto instructions ####
 
 
-#' @title Create instructions for giotto functions
-#' @name createGiottoInstructions
-#' @description Function to set global instructions for giotto functions
+#' @rdname giotto_instructions
 #' @param python_path path to python binary to use or directory one level
 #' up from the `env` directory (similar to output of 
 #' `reticulate::miniconda_path()`)
@@ -22,11 +20,6 @@
 #' @param fiji_path path to fiji executable
 #' @param no_python_warn turn off warning that no compatible python env has
 #' been detected
-#' @returns named vector with giotto instructions
-#' @seealso More online information can be found
-#' here \url{http://giottosuite.com}
-#' @examples
-#' createGiottoInstructions()
 #' @export
 createGiottoInstructions <- function(
     python_path = getOption("giotto.py_path"),
@@ -175,7 +168,13 @@ create_giotto_instructions <- function(python_path = NULL,
 }
 
 
-#' @title Read giotto instructions associated with giotto object
+
+# deprecated ####
+
+# These functions have been made internal. They will stop being exported
+# in a future version of GiottoClass
+
+#' @title deprecated
 #' @name readGiottoInstructions
 #' @description Retrieves the instruction associated with the provided parameter
 #' @param giotto_instructions giotto object or result from
@@ -190,9 +189,17 @@ create_giotto_instructions <- function(python_path = NULL,
 #'     param = "show_plot"
 #' )
 #' @export
+#' @keywords internal
 readGiottoInstructions <- function(giotto_instructions,
     param = NULL,
     default) {
+
+    deprecate_soft(
+        when = "0.3.5",
+        what = "readGiottoInstructions()",
+        with = "instructions()"
+    )
+
     # get instructions if provided the giotto object
     if (inherits(giotto_instructions, "giotto")) {
         giotto_instructions <- giotto_instructions@instructions
@@ -213,7 +220,7 @@ readGiottoInstructions <- function(giotto_instructions,
 }
 
 
-#' @title Show giotto instructions associated with giotto object
+#' @title deprecated
 #' @name showGiottoInstructions
 #' @description Function to display all instructions from giotto object
 #' @param gobject giotto object
@@ -223,13 +230,21 @@ readGiottoInstructions <- function(giotto_instructions,
 #'
 #' showGiottoInstructions(g)
 #' @export
+#' @keywords internal
 showGiottoInstructions <- function(gobject) {
+
+    deprecate_soft(
+        when = "0.3.5",
+        what = "showGiottoInstructions()",
+        with = "instructions()"
+    )
+
     instrs <- gobject@instructions
     return(instrs)
 }
 
 
-#' @title Change giotto instruction(s) associated with giotto object
+#' @title deprecated
 #' @name changeGiottoInstructions
 #' @description Function to change one or more instructions from giotto object.
 #' If more than one item is supplied to \code{params} and \code{new_values}, use
@@ -248,11 +263,20 @@ showGiottoInstructions <- function(gobject) {
 #'     new_values = TRUE
 #' )
 #' @export
+#' @keywords internal
 changeGiottoInstructions <- function(gobject,
     params = NULL,
     new_values = NULL,
     return_gobject = TRUE,
     init_gobject = TRUE) {
+
+    deprecate_soft(
+        when = "0.3.5",
+        what = "changeGiottoInstructions()",
+        with = "instructions()"
+    )
+
+
     instrs <- gobject@instructions
 
     if (is.null(params) | is.null(new_values)) {
@@ -263,10 +287,6 @@ changeGiottoInstructions <- function(gobject,
         stop("\t length of params need to be the same as new values \t")
     }
 
-    # if(!all(params %in% names(instrs))) {
-    #   stop('\t all params need to be part of Giotto instructions \t')
-    # }
-
     ## swap with new values
     instrs[params] <- new_values
 
@@ -289,7 +309,7 @@ changeGiottoInstructions <- function(gobject,
     })
 
     names(new_instrs) <- names(instrs)
-
+    class(new_instrs) <- "giottoInstructions"
 
 
     if (isTRUE(return_gobject)) {
@@ -303,7 +323,7 @@ changeGiottoInstructions <- function(gobject,
 
 
 
-#' @title Replace all giotto instructions in giotto object
+#' @title deprecated
 #' @name replaceGiottoInstructions
 #' @description Function to replace all instructions from giotto object. Does
 #' not call \code{initialize} on the giotto object
@@ -321,9 +341,17 @@ changeGiottoInstructions <- function(gobject,
 #'     instructions = createGiottoInstructions()
 #' )
 #' @export
+#' @keywords internal
 replaceGiottoInstructions <- function(gobject,
     instructions = NULL,
     init_gobject = TRUE) {
+
+    deprecate_soft(
+        when = "0.3.5",
+        what = "replaceGiottoInstructions()",
+        with = "instructions()"
+    )
+
     instrs_needed <- names(create_giotto_instructions())
 
     # validate new instructions
@@ -338,3 +366,15 @@ replaceGiottoInstructions <- function(gobject,
         return(gobject)
     }
 }
+
+
+# internals ####
+
+#' @export
+print.giottoInstructions <- function(x, ...) {
+    cat(sprintf("<%s>\n", class(x)[1]))
+    print_list(x)
+}
+
+
+