Merge branch 'master' into issue-297

.github/workflows/check-standard.yaml

@@ -0,0 +1,58 @@
+# 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:
+  workflow_dispatch:
+  pull_request:
+
+name: check-standard
+
+permissions: read-all
+
+jobs:
+  check-standard:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+            local::.
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual","--no-build-vignettes","--no-examples")'
+          build_args: 'c("--no-manual","--no-build-vignettes", "--no-resave-data")'
+          error-on: '"error"'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nichenetr
 Type: Package
 Title: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes
-Version: 2.1.5
+Version: 2.1.7
 Authors@R: c(person("Robin", "Browaeys",  role = c("aut")),
             person("Chananchida", "Sang-aram", role = c("aut", "cre"), email = "[email protected]"))
 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.
@@ -12,6 +12,7 @@ URL: https://github.com/saeyslab/nichenetr
 BugReports: https://github.com/saeyslab/nichenetr/issues
 RoxygenNote: 7.3.1
 Depends: R (>= 3.0.0)
+biocViews:
 Imports:
     tidyverse,
     data.table,
@@ -27,7 +28,6 @@ Imports:
     fdrtool,
     ROCR,
     caTools,
-    limma,
     Hmisc,
     caret,
     randomForest,
@@ -52,6 +52,7 @@ Suggests:
     rmarkdown,
     testthat,
     doMC,
+    limma,
     mco,
     parallel,
     covr,

NAMESPACE

@@ -185,7 +185,6 @@ importFrom(igraph,get.data.frame)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,page_rank)
 importFrom(igraph,sample_degseq)
-importFrom(limma,wilcoxGST)
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,reduce)

R/characterization_data_sources.R

@@ -353,10 +353,15 @@ evaluate_model = function(parameters_setting, lr_network, sig_network, gr_networ
   ligand_importances$spearman[is.na(ligand_importances$spearman)] = 0
   ligand_importances$pearson_log_pval[is.na(ligand_importances$pearson_log_pval)] = 0
   ligand_importances$spearman_log_pval[is.na(ligand_importances$spearman_log_pval)] = 0
-  ligand_importances$mean_rank_GST_log_pval[is.na(ligand_importances$mean_rank_GST_log_pval)] = 0
   ligand_importances$pearson_log_pval[is.infinite(ligand_importances$pearson_log_pval)] = 10000
   ligand_importances$spearman_log_pval[is.infinite(ligand_importances$spearman_log_pval)] = 10000
-  ligand_importances$mean_rank_GST_log_pval[is.infinite(ligand_importances$mean_rank_GST_log_pval)] = 10000
+
+  if ("mean_rank_GST_log_pval" %in% colnames(ligand_importances)){
+    ligand_importances$mean_rank_GST_log_pval[is.na(ligand_importances$mean_rank_GST_log_pval)] = 0
+    ligand_importances$mean_rank_GST_log_pval[is.infinite(ligand_importances$mean_rank_GST_log_pval)] = 10000
+  } else{
+    warning("mean_rank_GST_log_pval not in ligand_importances; do you have limma installed?")
+  }
 
   all_importances = ligand_importances %>% select_if(.predicate = function(x){sum(is.na(x)) == 0})
   # all_importances = full_join(ligand_importances, ligand_importances_glm, by = c("setting","test_ligand","ligand")) %>% full_join(ligand_importances_discrete, by = c("setting","test_ligand", "ligand"))