Fix r cmd check - I think...

Author: patrickCNMartin

.github/workflows/R-CMD-check.yaml

@@ -1,63 +1,37 @@
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
 
 name: R CMD Check
 
 permissions: read-all
 
 jobs:
-  
   check-package:
-    
     runs-on: ubuntu-latest
 
-    # Run checks with R-release, R-devel, and R-oldrelease.
-    strategy:
-      # Make sure each job runs independently. When `fail-fast` is true 
-      # (by default) all jobs in the matrix are cancelled as soon as one fails.
-      fail-fast: false
-      matrix:
-        r-version: ['release', 'devel', 'oldrel']
-
-    # Override the default job name to display the current R version name in
-    # parentheses (e.g. "check-package (R-release)").
-    name: "check-package (R-${{ matrix.r-version }})"
-
     steps:
-      # Pull the latest changes from the repository down to the runner.
       - name: Checkout
         uses: actions/checkout@v4
 
-      # Install R and any system dependencies.
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.r-version }}
           use-public-rspm: true
-          
-      
-      # Install R dependencies.
-      - name: Install Dependencies
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libbz2-dev liblzma-dev zlib1g-dev libglpk-dev pandoc texlive-latex-recommended texlive-latex-extra
+
+      - name: Install R dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: 
+          extra-packages: |
             any::rcmdcheck
-            any::pkgdown
-          # Installed packages are cached by default - force an upgrade to the 
-          # latest version of all dependencies.
+            cran::BiocManager
           upgrade: 'TRUE'
-      
-      # Run CRAN checks - fails if any ERRORs or WARNINGs are raised in which 
-      # case the `rcmdcheck` output will be uploaded as an artifact.
-      - name: Run Checks
-        uses: r-lib/actions/check-r-package@v2
-        env:
-            _R_CHECK_PKG_SIZES_: true
-            _R_CHECK_RD_XREFS_: true
-            _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: true
-            _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true
+
+      - name: Run checks
+        uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -1,30 +1,20 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
 
-name: pkgdown.yaml
+name: pkgdown
 
-permissions: read-all
+permissions:
+  contents: write
+  pages: write
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        r-version: ['release', 'devel', 'oldrel']
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
-    
+
     steps:
       - uses: actions/checkout@v4
 
@@ -33,17 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-    
-      
-      - name: Install Dependencies
+
+      - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: 
-            any::rcmdcheck
+          extra-packages: |
             any::pkgdown
           upgrade: 'TRUE'
 
-
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
@@ -54,4 +41,4 @@ jobs:
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: docs

DESCRIPTION

@@ -79,17 +79,17 @@ Imports:
     ggnewscale,
     kohonen,
     Rcpp,
-    RcppEigen,
-    TreeDist
+    TreeDist,
+    NMF
 Suggests:
     knitr,
     RUnit,
     rmarkdown,
     testthat (>= 3.0.0),
-    NMF,
     sf
 Encoding: UTF-8
 LazyData: true
+LazyDataCompression: bzip2
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 URL: https://patrickcnmartin.github.io/Vesalius/, https://github.com/patrickCNMartin/Vesalius, https://wonlab-cs.github.io/Vesalius/

NAMESPACE

@@ -43,6 +43,8 @@ importFrom(DESeq2,DESeqDataSetFromMatrix)
 importFrom(DESeq2,results)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,rowMeans)
+importFrom(NMF,coefficients)
+importFrom(NMF,nmf)
 importFrom(RANN,nn2)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(Rcpp,sourceCpp)
@@ -158,8 +160,11 @@ importFrom(patchwork,wrap_plots)
 importFrom(purrr,map)
 importFrom(purrr,map_dbl)
 importFrom(sp,point.in.polygon)
+importFrom(stats,IQR)
+importFrom(stats,as.dist)
 importFrom(stats,as.formula)
 importFrom(stats,chisq.test)
+importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,ecdf)
 importFrom(stats,fisher.test)
@@ -171,7 +176,11 @@ importFrom(stats,model.matrix)
 importFrom(stats,na.exclude)
 importFrom(stats,p.adjust)
 importFrom(stats,quantile)
+importFrom(stats,runif)
+importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,t.test)
+importFrom(stats,var)
 importFrom(stats,wilcox.test)
 importFrom(tools,toTitleCase)
 importFrom(tvR,denoise2)

R/dispatch.R

@@ -146,10 +146,12 @@ dispatch_sample <- function(territory_barcodes, ter, sample) {
 
 #' dispatch barcodes to subset cost for match clustering
 #' @param vesalius_assay vesalius_assay object post cell mapping
-#' @param cell_label character - name of column containing cell names
-#' if the clustering is to be done by cell types only
+#' @param cost cost matrix
+#' @param trial character - trial name
 #' @param group_identity character - name of column containing group
 #' to be used for cluster (i.e. territories, segments, layers etc)
+#' @param ref_cells character vector - reference cell barcodes
+#' @param query_cells character vector - query cell barcodes
 #' @return character string of barcodes
 dispatch_cost_groups <- function(vesalius_assay,
     cost,

R/embeddings.R

@@ -270,6 +270,7 @@ embed_latent_space <- function(counts,
 #' @return normalised PCA embedding matrix 
 #' @importFrom Seurat RunPCA
 #' @importFrom Seurat Embeddings
+#' @importFrom stats setNames
 embed_pca <- function(counts,
   dimensions,
   features = NULL,
@@ -503,27 +504,30 @@ embed_lsi_umap <- function(counts,
 #' @param counts Seurat object containing normalised counts
 #' @param dimensions number dimension to retain from NMF
 #' @param verbose logical if progress messages should be outputed
+#' @importFrom NMF nmf coefficients
 #' @return normalised NMF embedding matrix 
 embed_nmf <- function(counts, dimensions, verbose = TRUE) {
-  #--------------------------------------------------------------------------#
-  # adding this since I don't want to have this package as a dependancy 
-  # The problem is that those functions are exported to name space
-  # but NMF only works if the package is attached.
-  #--------------------------------------------------------------------------#
-  inst <- requireNamespace("NMF", quietly = TRUE)
-  if (!inst) {
-      stop("NMF is not installed - Please install NMF
-      install.packages('NMF')
-      https://cran.r-project.org/web/packages/NMF/index.html")
-  } else {
-      library("NMF")
-  }
+#   #--------------------------------------------------------------------------#
+#   # adding this since I don't want to have this package as a dependancy 
+#   # The problem is that those functions are exported to name space
+#   # but NMF only works if the package is attached.
+#   #--------------------------------------------------------------------------#
+#   inst <- requireNamespace("NMF", quietly = TRUE)
+#   if (!inst) {
+#       stop("NMF is not installed - Please install NMF
+#       install.packages('NMF')
+#       https://cran.r-project.org/web/packages/NMF/index.html")
+    
+#   } else {
+#       library("NMF")
+#   }
+
 
   #--------------------------------------------------------------------------#
   # Get the normalized count matrix and matrix with variable features 
   # from the Seurat object
   #--------------------------------------------------------------------------#
-  vesalius:::message_switch("nmf_tensor", verbose)
+  message_switch("nmf_tensor", verbose)
   features <- check_features(counts)
   count_matrix <- as.matrix(Seurat::GetAssayData(counts, layer = "data"))
   count_matrix <- count_matrix[features, ]
@@ -539,7 +543,7 @@ embed_nmf <- function(counts, dimensions, verbose = TRUE) {
   # Get the NMF projections (W matrix) and normalize
   #--------------------------------------------------------------------------#
   nmf_projections <- t(NMF::coefficients(nmf_result))
-  nmf_projections <- apply(nmf_projections, 2, vesalius:::norm_pixel, "minmax")
+  nmf_projections <- apply(nmf_projections, 2, norm_pixel, "minmax")
   nmf_projections <- list(as.matrix(nmf_projections))
   names(nmf_projections) <- "NMF"
 

R/equalize_image.R

@@ -5,7 +5,7 @@
 #' @param dimensions numeric vector of latent space dimensions to use.
 #' @param embedding character string describing which embedding should
 #' be used.
-#' @param type character - histogram EQ type. Select from: BalanceSimplest,
+#' @param method character - histogram EQ type. Select from: BalanceSimplest,
 #' EqualizePiecewise, SPE, EqualizeDP, EqualizeADP, ECDF (see details)
 #' @param N numeric describing how each colour channel will be mapped back to
 #' the image (Higher N = Higher greyscale contrast).

R/global_bindings.R

@@ -7,4 +7,5 @@ utils::globalVariables(c(".", "barcodes", "cc",
   "cc.y", "cluster", "p.value", "seurat_clusters",
   "territories", "territorries", "territory",
   "tile", "tmpImg", "value", "x", "y", "img", "p_value_adj",
-  "ind1", "ind2", "origin", "trial", "vesalius"))
+  "ind1", "ind2", "origin", "trial", "vesalius",
+  "c.1", "c.2", "c.3", "rgb_val","seed","query"))

R/integration.R

@@ -24,8 +24,11 @@
 #' should be merged with the reference data (see details)
 #' @param labels_reference character - which columns in the reference data assay
 #' should be merged with the mapped data (see details)
-#' @param regenerate_tiles logical - should tiles be regenrated from integrated 
+#' @param regenerate_tiles logical - should tiles be regenrated from integrated
 #' coordinates
+#' @param tensor_resolution numeric - tensor resolution for tile generation
+#' @param filter_grid numeric - filter grid parameter
+#' @param filter_threshold numeric - filter threshold parameter
 #' @param verbose logical - should progressed message be printed
 #' @details After mapping coordinates from a query onto a reference, vesalius
 #' provides a way to then integrate the assays together. This function will:
@@ -311,6 +314,7 @@ merge_coordinates <- function(matched, reference, barcodes) {
 #' to cell present in the other data set (similar to left and right joins).
 #' @return territory data frame with merged columns 
 #' @importFrom dplyr right_join
+#' @importFrom stats runif
 merge_territories <- function(matched,
     reference,
     coordinates,

R/isolate_territories.R

@@ -295,6 +295,7 @@ distance_pooling <- function(img, capture_radius, min_spatial_index) {
 #' @importFrom imager imsplit  threshold split_connected where
 #' @importFrom imagerExtra ThresholdML
 #' @importFrom dplyr inner_join
+#' @importFrom stats cor
 select_similar <- function(img,
   coordinates,
   threshold = 1) {