Merge pull request #138 from jiajic/dev

v0.1.2

.github/workflows/dev_check.yml

@@ -31,6 +31,9 @@ jobs:
       - name: Checkout repo for workflow access
         uses: actions/checkout@v3
 
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
       - name: Set up R environment
         uses: r-lib/actions/setup-r@v2
         with:
@@ -43,14 +46,7 @@ jobs:
           _R_CHECK_RD_XREFS: false
         with:
           dependencies: '"hard"' # do not use suggested dependencies
-          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::sp, any::stars, any::raster, any::sf
-
-      - name: Set up dependencies (GiottoData)
-        run: |
-          suppressWarnings({
-            remotes::install_github('drieslab/GiottoData', build = FALSE)
-          })
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::sp, any::stars, any::raster, any::sf, any::scattermore, any::exactextractr, github::drieslab/GiottoData
 
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),
@@ -34,7 +34,7 @@ Imports:
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     deldir (>= 1.0.6),
-    GiottoUtils (>= 0.1.0.1),
+    GiottoUtils (>= 0.1.2),
     igraph (>= 1.2.4.1),
     magick,
     Matrix (>= 1.6.2),
@@ -54,11 +54,13 @@ Suggests:
     geometry,
     GiottoData,
     HDF5Array (>= 1.18.1),
+    knitr,
     R.utils,
     raster,
     remotes,
     rhdf5,
     rlang,
+    rmarkdown,
     RTriangle (>= 1.6-0.10),
     S4Vectors,
     ScaledMatrix,
@@ -135,3 +137,4 @@ Collate:
     'suite_reexports.R'
     'zzz.R'
 URL: https://drieslab.github.io/GiottoClass/
+VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,dimObj)
+S3method(.DollarNames,metaData)
+S3method(.DollarNames,spatEnrObj)
+S3method(.DollarNames,spatLocsObj)
+S3method(.DollarNames,terraVectData)
 S3method(as.data.table,SpatVector)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
@@ -107,6 +112,7 @@ export(getExpression)
 export(getFeatureInfo)
 export(getFeatureMetadata)
 export(getGiottoImage)
+export(getMonochromeColors)
 export(getMultiomics)
 export(getNearestNetwork)
 export(getPolygonInfo)
@@ -368,6 +374,7 @@ importFrom(methods,show)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(methods,validObject)
+importFrom(utils,.DollarNames)
 importMethodsFrom(Matrix,t)
 importMethodsFrom(terra,"ext<-")
 importMethodsFrom(terra,as.data.frame)

NEWS.md

@@ -1,5 +1,19 @@
 
-# Giotto Class 0.1.1 (2023/12/16)
+# GiottoClass 0.1.2 (2024/01/02)
+
+## Added
+- Added: `max_window` and `colors` slots to `giottoLargeImage`. Use `GiottoClass:::.update_giotto_image()` to update outdated objects.
+- Added: `.bitdepth()` internal function to detect image bitdepth from sampled values
+- Added: re-export `getMonochromeColors()` from *GiottoUtils*
+- Added: `giottoPolygon`, `giottoLargeImage` method for `calculateOverlap()`
+- Added: vignette for working with spatial classes
+- Added: `output` param to `.spatraster_sample_values()`. Can now return as sampled `data.frame`, `array`, `magick`, `EBImage`
+
+## Changes
+- Fixes: Updates to raster `calculateOverlap()` workflows
+
+
+# GiottoClass 0.1.1 (2023/12/16)
 
 ## Breaking Changes
 - Removed: `getRainbowColors()` to *GiottoUtils*
@@ -24,7 +38,9 @@
 - Changed: `giottoPolygon` `plot()` now automatically switches to centroid plotting with more than 1e4 polys
 - Changed: Package internal functions now have `.` prefix
 
-# Giotto Class 0.1.0 (23/11/29)
+
+
+# GiottoClass 0.1.0 (2023/11/29)
 
 ## Breaking Changes
 

R/aggregate.R

@@ -295,6 +295,31 @@ setMethod(
 )
 
 
+# * giottoPolygon giottoLargeImage ####
+#' @rdname calculateOverlap
+#' @export
+setMethod(
+  "calculateOverlap", signature(x = "giottoPolygon", y = "giottoLargeImage"),
+  function(
+    x, y,
+    name_overlap = NULL,
+    poly_subset_ids = NULL,
+    return_gpolygon = TRUE,
+    verbose = TRUE,
+    ...
+  ) {
+    calculateOverlap(
+      x = x,
+      y = y@raster_object,
+      name_overlap = objName(y),
+      poly_subset_ids = poly_subset_ids,
+      verbose = verbose,
+      ...
+    )
+  }
+)
+
+
 # * giottoPolygon SpatRaster ####
 #' @rdname calculateOverlap
 #' @export
@@ -307,6 +332,10 @@ setMethod(
       return_gpolygon = TRUE,
       verbose = TRUE,
       ...) {
+    if (is.null(name_overlap)) {
+      .gstop("calculateOverlap: name_overlap must be given")
+    }
+
     res <- calculateOverlap(
       x = x[],
       y = y,
@@ -1189,13 +1218,20 @@ setMethod(
       )
     }
 
-    # pass to SpatVector method
-    overlapToMatrix(
+    argslist <- list(
       x = overlaps_data,
       count_info_column = count_info_column,
       output = output,
       ...
     )
+
+    # this arg not accepted by method
+    if (type == "intensity") {
+      argslist$count_info_column <- NULL
+    }
+
+    # pass to SpatVector method
+    do.call(overlapToMatrix, args = argslist)
   }
 )
 

R/classes.R

@@ -428,6 +428,11 @@ updateGiottoObject <- function(gobject) {
     gobject@h5_file <- NULL
   }
 
+  # GiottoClass 0.1.2 adds max_window and colors slots to giottoLargeImage
+  if (!is.null(gobject@largeImages)) {
+    gobject@largeImages <- lapply(gobject@largeImages, .update_giotto_image)
+  }
+
   # # 3.3.X release adds mirai slot
   # if (is.null(attr(gobject, "mirai"))) {
   #   attr(gobject, "mirai") <- list()
@@ -1464,8 +1469,10 @@ giottoImage <- setClass(
 #' @slot overall_extent terra extent object covering the original extent of image
 #' @slot scale_factor image scaling relative to spatial locations
 #' @slot resolution spatial location units covered per pixel
-#' @slot max_intensity value to set as maximum intensity in color scaling
-#' @slot min_intensity minimum value found
+#' @slot max_intensity approximate maximum value
+#' @slot min_intensity approximate minimum value
+#' @slot max_window value to set as maximum intensity in color scaling
+#' @slot colors color mappings in hex codes
 #' @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
@@ -1476,12 +1483,14 @@ giottoLargeImage <- setClass(
   slots = c(
     name = "ANY",
     raster_object = "ANY",
-    extent = "ANY",
-    overall_extent = "ANY",
+    extent = "ANY", # REMOVE?
+    overall_extent = "ANY", # REMOVE? New slot px_dims as replacement?
     scale_factor = "ANY",
     resolution = "ANY",
-    max_intensity = "ANY",
-    min_intensity = "ANY",
+    max_intensity = "numeric",
+    min_intensity = "numeric",
+    max_window = "numeric", # NEW
+    colors = 'character', # NEW
     is_int = "ANY",
     file_path = "ANY",
     OS_platform = "ANY"
@@ -1493,10 +1502,55 @@ giottoLargeImage <- setClass(
     overall_extent = NULL,
     scale_factor = NULL,
     resolution = NULL,
-    max_intensity = NULL,
-    min_intensity = NULL,
+    max_intensity = NA_real_,
+    min_intensity = NA_real_,
+    max_window = NA_real_,
+    colors = grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1),
     is_int = NULL,
     file_path = NULL,
     OS_platform = NULL
   )
 )
+
+# function for updating image objects if structure definitions have changed
+.update_giotto_image = function(x) {
+  # 0.1.2 release adds colors & max_window slots
+  if (is.null(attr(x, "colors"))) {
+    attr(x, "colors") <- grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1)
+  }
+  if (is.null(attr(x, "max_window"))) {
+    # get a max intensity value
+    if (!is.null(x@max_intensity)) {
+      x@max_intensity <- .spatraster_intensity_range(x@raster_object)[["max"]]
+    }
+
+    attr(x, "max_window") <- .bitdepth(x@max_intensity, return_max = TRUE)
+  }
+
+  # 0.1.x release adds giottoImageStack
+  # deprecate
+
+  return(x)
+}
+
+
+
+## giottoImageStack class ####
+
+## * definition ####
+# giottoImageStack class
+
+# giottoImageStack <- setClass(
+#   Class = "giottoImageStack",
+#
+#   slots = c(
+#     name = 'character',
+#     images = 'giottoLargeImage',
+#     weight = 'numeric'
+#   )
+# )
+
+
+
+
+

R/create.R

@@ -2840,7 +2840,10 @@ createGiottoLargeImage <- function(raster_object,
   ## 6. extent object
   g_imageL@extent <- g_imageL@overall_extent <- as.vector(terra::ext(raster_object))
 
-  ## 7. return image object
+  ## 7. Assign discovered bitdepth max value as max window
+  g_imageL@max_window <- .bitdepth(g_imageL@max_intensity, return_max = TRUE)
+
+  ## 8. return image object
   return(g_imageL)
 }