Merge pull request #44 from jiajic/master

Merge suite_modular into master

.Rbuildignore

@@ -1,2 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -5,3 +5,4 @@
 .RData
 .Ruserdata
 *.DS_Store
+docs

DESCRIPTION

@@ -1,25 +1,33 @@
 Package: GiottoData
 Type: Package
 Title: Datasets for Giotto
-Version: 0.2.5
+Version: 0.2.6.2
 Author: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"))
 		 )
 Maintainer: Ruben Dries <rubendries@gmail.com>
 Description: Stores information and scripts to work with, or load various
     different spatial datasets that can be used with the Giotto Suite workflow.
-    Also contains example mini Giotto subobjects
+    Also contains example mini Giotto subobjects.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://drieslab.github.io/GiottoData/, https://github.com/drieslab/GiottoData
 BugReports: https://github.com/drieslab/GiottoData/issues
 Depends:
     R (>= 3.5.0),
-    Giotto (>= 3.0.0)
+    GiottoClass,
+    GiottoUtils,
+    utils (>= 3.5.0)
 Imports:
-    utils (>= 3.5.0),
     data.table (>= 1.14.0),
+Suggests:
+    GiottoVisuals,
+    Giotto,
     terra (>= 1.5-12)
+Remotes:
+    drieslab/GiottoClass,
+    drieslab/GiottoUtils,
+    drieslab/Giotto@suite_modular
 RoxygenNote: 7.2.3

NAMESPACE

@@ -8,6 +8,9 @@ export(listSODBDatasetNames)
 export(listSubObjectMini)
 export(loadGiottoMini)
 export(loadSubObjectMini)
+import(GiottoClass)
+import(GiottoUtils)
 import(data.table)
 import(ggplot2)
 import(utils)
+importClassesFrom(data.table,data.table)

R/dataset_helpers.R

@@ -23,51 +23,34 @@ loadGiottoMini = function(dataset = c('visium', 'seqfish', 'starmap', 'vizgen',
 
   dataset = match.arg(dataset, choices = c('visium', 'seqfish', 'starmap', 'vizgen', 'cosmx', 'spatialgenomics'))
 
-
-  if(dataset == 'visium') {
-    mini_gobject = Giotto::loadGiotto(path_to_folder = system.file('/Mini_datasets/Visium/VisiumObject/', package = 'GiottoData'),
-                                      python_path = python_path,
-                                      reconnect_giottoImage = FALSE)
-  }
-
-
-  if(dataset == 'vizgen') {
-    mini_gobject = Giotto::loadGiotto(path_to_folder = system.file('/Mini_datasets/Vizgen/VizgenObject/', package = 'GiottoData'),
-                              python_path = python_path,
-                              reconnect_giottoImage = FALSE)
-  }
-
-  if(dataset == 'cosmx') {
-    mini_gobject = Giotto::loadGiotto(path_to_folder = system.file('/Mini_datasets/CosMx/CosMxObject/', package = 'GiottoData'),
-                                      python_path = python_path,
-                                      reconnect_giottoImage = FALSE)
-  }
-
-
-  if(dataset == 'seqfish') {
-    Giotto:::wrap_msg('To be implemented \n')
-  }
-
-  if(dataset == 'starmap') {
-    mini_gobject = Giotto::loadGiotto(path_to_folder = system.file('/Mini_datasets/3D_starmap/3DStarmapObject/', package = 'GiottoData'),
-                              python_path = python_path)
-    }
-
-  if(dataset == 'spatialgenomics') {
-    mini_gobject = Giotto::loadGiotto(path_to_folder = system.file('/Mini_datasets/SpatialGenomics/SpatialGenomicsObject/', package = 'GiottoData'),
-                              python_path = python_path)
-  }
+  mini_gobject = switch(
+    dataset,
+    'visium' = loadGiotto(path_to_folder = system.file('/Mini_datasets/Visium/VisiumObject/', package = 'GiottoData'),
+                          python_path = python_path,
+                          reconnect_giottoImage = FALSE),
+    'vizgen' = loadGiotto(path_to_folder = system.file('/Mini_datasets/Vizgen/VizgenObject/', package = 'GiottoData'),
+                          python_path = python_path,
+                          reconnect_giottoImage = FALSE),
+    'cosmx' = loadGiotto(path_to_folder = system.file('/Mini_datasets/CosMx/CosMxObject/', package = 'GiottoData'),
+                         python_path = python_path,
+                         reconnect_giottoImage = FALSE),
+    'seqfish' = {
+      wrap_msg('To be implemented \n')
+      return(invisible(NULL)) # exit early
+    },
+    'starmap' = loadGiotto(path_to_folder = system.file('/Mini_datasets/3D_starmap/3DStarmapObject/', package = 'GiottoData'),
+                           python_path = python_path),
+    'spatialgenomics' = loadGiotto(path_to_folder = system.file('/Mini_datasets/SpatialGenomics/SpatialGenomicsObject/', package = 'GiottoData'),
+                                   python_path = python_path)
+  )
 
 
   # 1. change default instructions
-  identified_python_path = set_giotto_python_path(python_path = python_path)
-  print(identified_python_path)
+  # Only mini object-specific instructions should be updated here. The python
+  # path update was taken care of inside of `loadGiotto()`
   mini_gobject = changeGiottoInstructions(gobject = mini_gobject,
                                           params = c('show_plot', 'return_plot', 'save_plot', 'save_dir'),
-                                          new_values = c(TRUE, FALSE, FALSE, NA)
-                                          #params = c('python_path', 'show_plot', 'return_plot', 'save_plot', 'save_dir'),
-                                          #new_values = c(identified_python_path, TRUE, FALSE, FALSE, getwd())
-                                          )
+                                          new_values = c(TRUE, FALSE, FALSE, NA))
 
   return(mini_gobject)
 
@@ -125,7 +108,7 @@ getSpatialDataset = function(dataset = c('ST_OB1',
                                                      'sg_mini_kidney'))
 
   # check operating system first
-  os_specific_system = Giotto:::get_os()
+  os_specific_system = get_os()
 
   #if(os_specific_system == 'windows') {
   #  stop('This function is currently not supported on windows systems,
@@ -169,20 +152,20 @@ getSpatialDataset = function(dataset = c('ST_OB1',
   selection = datasets_file[['dataset']] == sel_dataset
   selected_dataset_info = datasets_file[selection,]
   if(verbose) {
-    Giotto:::wrap_msg('Selected dataset links for: ', sel_dataset, ' \n \n')
+    wrap_msg('Selected dataset links for: ', sel_dataset, ' \n \n')
     print(selected_dataset_info)
   }
 
 
 
   # get url to expression matrix and download
   if(verbose) {
-    Giotto:::wrap_msg("\n \n Download expression matrix: \n")
+    wrap_msg("\n \n Download expression matrix: \n")
   }
   expr_matrix_url = selected_dataset_info[['expr_matrix']]
 
   if(expr_matrix_url == "") {
-    Giotto:::wrap_msg('\n No expression found, skip this step \n')
+    wrap_msg('\n No expression found, skip this step \n')
   } else {
 
     expr_matrix_url = unlist(strsplit(expr_matrix_url, split = '\\|'))
@@ -192,7 +175,7 @@ getSpatialDataset = function(dataset = c('ST_OB1',
       mydestfile = paste0(directory,'/', myfilename)
 
       if(dryrun) {
-        Giotto:::wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
+        wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
       } else {
         utils::download.file(url = url, destfile = mydestfile, ...)
       }
@@ -207,13 +190,13 @@ getSpatialDataset = function(dataset = c('ST_OB1',
 
   # get url to spatial locations and download
   if(verbose) {
-    Giotto:::wrap_msg("\n \n Download spatial locations: \n")
+    wrap_msg("\n \n Download spatial locations: \n")
   }
 
   spatial_locs_url = selected_dataset_info[['spatial_locs']]
 
   if(spatial_locs_url == "") {
-    Giotto:::wrap_msg('\n No spatial locations found, skip this step \n')
+    wrap_msg('\n No spatial locations found, skip this step \n')
   } else {
 
     spatial_locs_url = unlist(strsplit(spatial_locs_url, split = '\\|'))
@@ -223,7 +206,7 @@ getSpatialDataset = function(dataset = c('ST_OB1',
       mydestfile = paste0(directory,'/', myfilename)
 
       if(dryrun) {
-        Giotto:::wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
+        wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
       } else {
         utils::download.file(url = url, destfile = mydestfile, ...)
       }
@@ -236,14 +219,14 @@ getSpatialDataset = function(dataset = c('ST_OB1',
 
   # get url(s) to additional metadata files and download
   if(verbose) {
-    Giotto:::wrap_msg("\n \n Download metadata: \n")
+    wrap_msg("\n \n Download metadata: \n")
   }
 
   #metadata_url = selected_dataset_info[['metadata']][[1]]
   metadata_url = selected_dataset_info[['metadata']]
 
   if(metadata_url == "") {
-    Giotto:::wrap_msg('\n No metadata found, skip this step \n')
+    wrap_msg('\n No metadata found, skip this step \n')
   } else {
 
     metadata_url = unlist(strsplit(metadata_url, split = '\\|'))
@@ -253,7 +236,7 @@ getSpatialDataset = function(dataset = c('ST_OB1',
       mydestfile = paste0(directory,'/', myfilename)
 
       if(dryrun) {
-        Giotto:::wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
+        wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
       } else {
         utils::download.file(url = url, destfile = mydestfile, ...)
       }
@@ -269,11 +252,11 @@ getSpatialDataset = function(dataset = c('ST_OB1',
   spatial_seg_url = selected_dataset_info[['segmentations']]
 
   if(spatial_seg_url == "") {
-    # Giotto:::wrap_msg('\n No segmentations found, skip this step \n')
+    # wrap_msg('\n No segmentations found, skip this step \n')
   } else {
 
     if(verbose) {
-      Giotto:::wrap_msg("\n \n Download segmentations: \n")
+      wrap_msg("\n \n Download segmentations: \n")
     }
 
     spatial_seg_url = unlist(strsplit(spatial_seg_url, split = '\\|'))
@@ -283,7 +266,7 @@ getSpatialDataset = function(dataset = c('ST_OB1',
       mydestfile = paste0(directory,'/', myfilename)
 
       if(dryrun) {
-        Giotto:::wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
+        wrap_msg("utils::download.file(url = ", url, ", destfile = ", mydestfile, ", ...)")
       } else {
         utils::download.file(url = url, destfile = mydestfile, ...)
       }

R/package_imports.R

@@ -0,0 +1,5 @@
+#' @import GiottoClass
+#' @import GiottoUtils
+#' @importClassesFrom data.table data.table
+#' @import utils
+NULL

R/test_objects.R

@@ -8,6 +8,9 @@
 #' is available (see \code{\link{listSubObjectMini}})
 #' @export
 loadSubObjectMini = function(x, idx = 1L) {
+
+  # declare data.table variables
+  type = index = path = NULL
 
   avail_obj_dt = list_subobject_mini()
   data_path = avail_obj_dt[type == x & index == idx, path]
@@ -16,23 +19,23 @@ loadSubObjectMini = function(x, idx = 1L) {
 
   # wrapped objects
   if(x %in% c('giottoPoints', 'giottoPolygon')) {
-    load_data = terra::vect(load_data)
+    load_data = GiottoClass::vect(load_data)
   }
 
   if(x == 'giottoLargeImage') {
     original_path = load_data@file_path
     new_path = gsub(pattern = '.*[/]GiottoData/', replacement = '', x = original_path)
     new_path = paste0(gDataDir(), new_path)
-    load_data = Giotto:::reconnect_giottoLargeImage(giottoLargeImage = load_data,
-                                                    image_path = new_path)
+    load_data = GiottoClass::reconnect_giottoLargeImage(giottoLargeImage = load_data,
+                                                        image_path = new_path)
   }
 
   if(x == 'giottoImage') {
     original_path = load_data@file_path
     new_path = gsub(pattern = '.*[/]GiottoData/', replacement = '', x = original_path)
     new_path = paste0(gDataDir(), new_path)
-    load_data = Giotto:::reconnect_giottoImage_MG(giottoImage = load_data,
-                                                  image_path = new_path)
+    load_data = GiottoClass::reconnect_giottoImage_MG(giottoImage = load_data,
+                                                      image_path = new_path)
   }
 
   return(load_data)
@@ -49,6 +52,9 @@ loadSubObjectMini = function(x, idx = 1L) {
 #' @param x subobject type (NULL lists all subobject types)
 #' @export
 listSubObjectMini = function(x = NULL) {
+
+  # declare data.table variables
+  path = type = NULL
 
   avail_obj_dt = list_subobject_mini()
   avail_obj_dt_show = copy(avail_obj_dt)[, path := NULL]
@@ -70,15 +76,18 @@ listSubObjectMini = function(x = NULL) {
 #' for the external version which provides those functions.
 #' @keywords internal
 list_subobject_mini = function() {
+
+  # declare data.table variables
+  path = type = NULL
 
   miniobj_path = paste0(gDataDir(), '/Mini_objects/subobjects')
 
   avail_obj = list.files(path = miniobj_path, full.names = TRUE, recursive = TRUE)
   avail_obj_dt = data.table::data.table(file = basename(avail_obj), path = avail_obj)
-  avail_obj_dt[, type := gsub(pattern = paste0(miniobj_path, '/'), replacement = '', x = path)]
-  avail_obj_dt[, type := gsub(pattern = '[/].*', replacement = '', x = type)]
+  avail_obj_dt[, 'type' := gsub(pattern = paste0(miniobj_path, '/'), replacement = '', x = path)]
+  avail_obj_dt[, 'type' := gsub(pattern = '[/].*', replacement = '', x = type)]
 
-  avail_obj_dt[, index := seq_along(path), by = type]
+  avail_obj_dt[, 'index' := seq_along(path), by = type]
 
   return(avail_obj_dt)
 

README.Rmd

@@ -5,8 +5,15 @@ output: github_document
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 <!-- This line is from RStudio -->
 
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/"
+)
+```
 
-# GiottoData
+# GiottoData <img src="man/figures/logo.png" align="right" alt="" width="160" />
 
 Repo for GiottoData