Giotto v4.0.4

- `createGiottoVisiumObject()` now generates `giottoLargeImages` instead of `giottoImage`. The `largeImage_name` param will need to be used in plotting functions for Visium following this update. Tutorials will also need to be updated to use this param in order to have the images show up.
RubD · Feb 29, 2024 · 7c6471c · 7c6471c
2 parents d66bc01 + b2cbb98
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,10 +7,12 @@
 ^README\.Rmd$
 ^CODE_OF_CONDUCT\.md$
 ^INDEX.md$
+^CNAME$
 
 ^docs
 ^vignettes
 ^\.github
+^testdata
 
 ^codecov\.yml$
 ^_pkgdown\.yml$

diff --git a/.github/workflows/covr.yml b/.github/workflows/covr.yml
@@ -23,7 +23,7 @@ jobs:
     steps:
 
       - name: Checkout repo for workflow access
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up R environment
         uses: r-lib/actions/setup-r@v2
@@ -37,16 +37,18 @@ 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::covr
+          install-pandoc: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::rlang
+            any::R.utils
+            any::covr
+            any::remotes
+            any::hdf5r
+            github::drieslab/GiottoData
           needs: coverage
 
-      - name: Set up dependencies (GiottoData)
-        run: |
-          suppressWarnings({
-            remotes::install_github('drieslab/GiottoData', build = FALSE)
-          })
-        shell: Rscript {0}
-
       - name: Generate coverage report
         run: |
           covr::codecov(

diff --git a/.github/workflows/lintr.yml b/.github/workflows/lintr.yml
@@ -33,7 +33,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up R environment
         uses: r-lib/actions/setup-r@v2

diff --git a/.github/workflows/main_check.yaml b/.github/workflows/main_check.yaml
@@ -42,7 +42,7 @@ jobs:
         shell: bash
 
       - name: Checkout repo for workflow access
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up R environment
         uses: r-lib/actions/setup-r@v2
@@ -58,13 +58,25 @@ 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::covr, any::spdep, any::future.apply, github::drieslab/GiottoData
+          install-pandoc: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::hdf5r
+            any::rlang
+            any::R.utils
+            any::remotes
+            any::spdep
+            any::future.apply
+            github::drieslab/GiottoData
 
       - name: Test python env install
         run: |
           if (!GiottoClass::checkGiottoEnvironment()) {
             GiottoClass::installGiottoEnvironment()
           }
+
+          reticulate::py_list_packages(envname = "giotto_env")
         shell: Rscript {0}
 
       - name: Run R CMD check

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.3
+Version: 4.0.4
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),
@@ -32,7 +32,7 @@ Depends:
     utils (>= 3.5.0),
     R (>= 3.5.0),
     methods,
-    GiottoClass (>= 0.1.1)
+    GiottoClass (>= 0.2.0)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -42,7 +42,7 @@ Imports:
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
     ggrepel,
-    GiottoUtils (>= 0.1.1),
+    GiottoUtils (>= 0.1.6),
     GiottoVisuals (>= 0.1.1),
     igraph (>= 1.2.4.1),
     jsonlite,

diff --git a/NEWS.md b/NEWS.md
@@ -1,20 +1,47 @@
+
+# Giotto 4.0.4
+
+## Breaking changes
+* Remove `do_manual_adj` and image adjustment params from `createGiottoVisiumObject()`
+* `createGiottoVisiumObject()` now creates `giottoLargeImage` for spatial images.
+* `exprCellCellcom()` deprecated `gene_set_*` params removed
+
+## Bug fixes
+* Fix metadata appending/sorting issues introduced by *GiottoClass v0.1.3* (2024/01/12). Affected functions: `addHMRF()`, `addFeatsPerc()`, `doScrubletDetect()`
+* `findNetworkNeighbors()` now has default `spatial_network_name` value of `NULL`
+* `get10Xmatrix()` now obeys `split_by_type = FALSE`
+
+## Changes
+* Deprecate `set.seed` in favor of `seed` param for `binSpect()`
+* `binSpect()` now sets a seed by default for reproducibility
+* pkgdown files moved to separate [repo](https://github.com/drieslab/Giotto_website)
+
+## Enhancements
+* Use `mixedsort()` for unique clusters metadata info
+* Remove unnecessary matrix densification and expose `seed` param in `doScrubletDetect()`
+* Remove unnecessary matrix densification in `makeSignMatrixRank()`
+
+
 # Giotto 4.0.3 (2024/02/20)
 
+
 ## Bug fixes
-- Remove old argument `type_default = list(pal = c('blue', 'yellow', 'red'))` in plotRankSpatvsExpr()
+* Remove old argument `type_default = list(pal = c('blue', 'yellow', 'red'))` in plotRankSpatvsExpr()
+
 
 # Giotto 4.0.2 (2023/12/21)
 
 ## Bug Fixes
-- fix bug in `doHclust()`
+* fix bug in `doHclust()`
 
 ## Changes
 * Move *GiottoClass* back to depends to fix access to some generics
 
+
 # Giotto 4.0.1 (2023/12/16)
 
-## Breaking Changes
-* Remove `cell_ids` param for `calculateHVF` in favor of simpler `random_subset`
+## Breaking changes
+* Remove `cell_ids` param for `calculateHVF()` in favor of simpler `random_subset`
 * Move *GiottoUtils*, *GiottoClass*, and *GiottoVisuals* to imports
 
 ## Added
@@ -32,7 +59,7 @@
 
 # Giotto 4.0.0 (2023/11/29)
 
-## Breaking Changes
+## Breaking changes
 * Update to modular package organization with the main packages being `GiottoUtils`, `GiottoClass`, `GiottoVisuals`, and `Giotto` as the analytical umbrella package.
 
 ## Added
@@ -55,7 +82,7 @@
 
 # Giotto 3.3.1 (2023/08/02)
 
-## Breaking Changes
+## Breaking changes
 
 * Change `checkGiottoEnvironment()`. Downgrade from error to message and return FALSE when a provided directory does not exist
 
@@ -110,7 +137,7 @@
 
 # Giotto 3.3.0 (2023/04/18)
 
-## Breaking Changes
+## Breaking changes
 
 * Set Suite as default branch
 * Removed all deprecated accessors from `accessors.R`
@@ -168,7 +195,7 @@
 
 # Giotto 3.2.0 (2023/02/02)
 
-## Breaking Changes
+## Breaking changes
 
 * Removed support for deprecated nesting in `@nn_network` slot
 * `createSpatialNetwork()` will now output a `spatialNetworkObj` by default when `return_gobject = FALSE`. It is possible to change this back to the data.table output by setting `output = 'data.table'`
@@ -254,7 +281,7 @@
 
 # Giotto 3.0.0 (2022/11/18)
 
-## Breaking Changes
+## Breaking changes
 
 * S4 subobjects framework will require giotto objects to be remade
 
@@ -279,7 +306,7 @@
 
 # Giotto 2.1.0 (2022/11/09)
 
-## Breaking Changes
+## Breaking changes
 
 * Update of python version to **3.10.2** [details](https://giottosuite.readthedocs.io/en/latest/additionalinformation.html#giotto*suite*2*1*0*2202*11*09)
 
@@ -316,7 +343,7 @@
 * Deprecate `combineInteractionChangedGenes()`, `combineICG()`, `combineCPG()` in favor of `combineInteractionChangedFeats()` and `combineICF()`
 * Deprecate `combineCellProximityGenes_per_interaction()` in favor of `combineCellProximityFeatures_per_interaction()`
 
-## Breaking Changes
+## Breaking changes
 
 * ICF output internal object structure names have changed to use feats instead of genes
 

diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R
@@ -1306,7 +1306,7 @@ addFeatStatistics <- function(gobject,
                               feat_type = feat_type,
                               spat_unit = spat_unit,
                               new_metadata = feat_stats,
-                              by_column = T,
+                              by_column = TRUE,
                               column_feat_ID = 'feats')
 
     ## update parameters used ##
@@ -1581,15 +1581,15 @@ addFeatsPerc = function(gobject,
 
   totalsum = colSums_flex(expr_data)
   feat_sum = colSums_flex(expr_data[rownames(expr_data) %in% feats,])
-  perc_feats = round((feat_sum/totalsum)*100, 2)
+  perc_feats = round((feat_sum/totalsum) * 100, 2)
 
-  if(return_gobject == TRUE) {
+  if(return_gobject) {
     temp_gobj = addCellMetadata(gobject = gobject,
                                 spat_unit = spat_unit,
                                 feat_type = feat_type,
                                 new_metadata = perc_feats,
                                 vector_name = vector_name,
-                                by_column = F)
+                                by_column = TRUE)
 
     ## update parameters used ##
     temp_gobj = update_giotto_params(temp_gobj, description = '_feats_perc')
@@ -1623,7 +1623,7 @@ addFeatsPerc = function(gobject,
 #' @export
 findNetworkNeighbors = function(gobject,
                                 spat_unit = NULL,
-                                spatial_network_name,
+                                spatial_network_name = NULL,
                                 source_cell_ids = NULL,
                                 name = 'nb_cells') {