simplified code in application_prediction.get_weighted_ligand_target_links

.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: 2.1.0
+Title: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet
+Version: 2.2.0
 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.
@@ -10,8 +10,9 @@ Encoding: UTF-8
 LazyData: true
 URL: https://github.com/saeyslab/nichenetr
 BugReports: https://github.com/saeyslab/nichenetr/issues
-RoxygenNote: 7.1.2
+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/application_prediction.R

@@ -129,10 +129,8 @@ get_weighted_ligand_target_links = function(ligand, geneset,ligand_target_matrix
   targets = intersect(ligand_target_matrix[,ligand] %>% .[. >= top_n_score ] %>% names(),geneset)
   if (length(targets) == 0){
     ligand_target_weighted_df = tibble(ligand = ligand, target = NA, weight = NA)
-  } else if (length(targets) == 1) {
-    ligand_target_weighted_df = tibble(ligand = ligand, target = targets, weight = ligand_target_matrix[targets,ligand])
   } else {
-    ligand_target_weighted_df = tibble(ligand = ligand, target = names(ligand_target_matrix[targets,ligand])) %>% inner_join(tibble(target = names(ligand_target_matrix[targets,ligand]), weight = ligand_target_matrix[targets,ligand]), by = "target")
+    ligand_target_weighted_df = tibble(ligand = ligand, target = targets, weight = ligand_target_matrix[targets,ligand])
   }
   return(ligand_target_weighted_df)
 }
@@ -2189,9 +2187,9 @@ get_lfc_celltype = function(celltype_oi, seurat_obj, condition_colname, conditio
   SeuratV4 = c("avg_log2FC") %in% colnames(DE_table_sender)
 
   if(SeuratV4 == TRUE){
-    DE_table_sender = DE_table_sender %>% as_tibble() %>% select(-p_val) %>% select(gene, avg_log2FC)
+    DE_table_sender = DE_table_sender %>% as_tibble() %>% select(gene, avg_log2FC)
   } else {
-    DE_table_sender = DE_table_sender %>% as_tibble() %>% select(-p_val) %>% select(gene, avg_logFC)
+    DE_table_sender = DE_table_sender %>% as_tibble() %>% select(gene, avg_logFC)
   }
 
   colnames(DE_table_sender) = c("gene",celltype_oi)