Merge pull request #201 from saeyslab/new-release

NicheNet v2

Author: browaeysrobin

.github/workflows/check-bioc.yml

@@ -20,9 +20,7 @@
 ## * GHA: GitHub Action
 ## * OS: operating system
 
-on:
-  push:
-  pull_request:
+on: workflow_dispatch
 
 name: R-CMD-check-bioc
 
@@ -56,6 +54,7 @@ jobs:
           - { os: windows-latest, r: '4.1', bioc: '3.13'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM_ROOT: https://packagemanager.posit.co.
       RSPM: ${{ matrix.config.rspm }}
       NOT_CRAN: true
       TZ: UTC
@@ -76,41 +75,41 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -126,6 +125,7 @@ jobs:
           sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
           echo $sysreqs
           sudo -s eval "$sysreqs"
+          
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
@@ -160,7 +160,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, update = FALSE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -178,6 +178,7 @@ jobs:
           BiocManager::install("ComplexHeatmap", update = FALSE)
           remotes::install_cran("circlize")
           remotes::install_cran("tidyverse")
+          remotes::install_cran("DiagrammeR", type = ifelse("${{ runner.os }}" == "Windows", "win.binary", getOption("pkgType")))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: nichenetr
 Type: Package
 Title: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes
-Version: 1.1.1
-Authors@R: person("Robin", "Browaeys", email = "robin.browaeys@ugent.be",
-  role = c("aut", "cre"))
+Version: 2.0.0
+Authors@R: c(person("Robin", "Browaeys",  role = c("aut")),
+            person("Chananchida", "Sang-aram", role = c("aut", "cre"), email = "chananchida.sangaram@ugent.be"))
 Description: This package allows you the investigate intercellular communication from a computational perspective. More specifically, it allows to investigate how interacting cells influence each other's gene expression. Functionalities of this package (e.g. including predicting extracellular upstream regulators and their affected target genes) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/saeyslab/nichenetr
 BugReports: https://github.com/saeyslab/nichenetr/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Depends: R (>= 3.0.0)
 Imports: 
     dplyr,
@@ -41,11 +41,16 @@ Imports:
     magrittr,
     circlize,
     ComplexHeatmap,
-    grDevices
-Suggests: knitr,
+    grDevices,
+    ggnewscale,
+    ggforce,
+    shadowtext
+Suggests: 
+    knitr,
     rmarkdown,
     testthat,
     doMC,
+    mco,
     parallel,
     covr,
     tidyverse

NAMESPACE

@@ -7,6 +7,7 @@ export(alias_to_symbol_seurat)
 export(apply_hub_corrections)
 export(assess_influence_source)
 export(assess_rf_class_probabilities)
+export(calculate_de)
 export(calculate_fraction_top_predicted)
 export(calculate_fraction_top_predicted_fisher)
 export(calculate_niche_de)
@@ -53,12 +54,14 @@ export(extract_top_fraction_ligands)
 export(extract_top_fraction_targets)
 export(extract_top_n_ligands)
 export(extract_top_n_targets)
+export(generate_prioritization_tables)
 export(get_active_ligand_receptor_network)
 export(get_active_ligand_target_df)
 export(get_active_ligand_target_matrix)
 export(get_active_regulatory_network)
 export(get_active_signaling_network)
 export(get_expressed_genes)
+export(get_exprs_avg)
 export(get_lfc_celltype)
 export(get_ligand_activities_targets)
 export(get_ligand_signaling_path)
@@ -88,6 +91,7 @@ export(make_heatmap_ggplot)
 export(make_ligand_activity_target_exprs_plot)
 export(make_ligand_receptor_lfc_plot)
 export(make_ligand_receptor_lfc_spatial_plot)
+export(make_mushroom_plot)
 export(make_threecolor_heatmap_ggplot)
 export(mlrmbo_optimization)
 export(model_based_ligand_activity_prediction)
@@ -115,6 +119,7 @@ export(process_mlrmbo_nichenet_optimization)
 export(process_niche_de)
 export(process_receiver_target_de)
 export(process_spatial_de)
+export(process_table_to_ic)
 export(randomize_complete_network_source_specific)
 export(randomize_datasource_network)
 export(randomize_network)
@@ -128,10 +133,14 @@ export(wrapper_average_performances)
 export(wrapper_evaluate_single_importances_ligand_prediction)
 import(Seurat)
 import(caret)
+import(cowplot)
 import(dplyr)
 import(e1071)
+import(ggforce)
+import(ggnewscale)
 import(ggplot2)
 import(readr)
+import(shadowtext)
 import(tibble)
 import(tidyr)
 importFrom(ComplexHeatmap,Legend)