Add webpage multideconv

Add vignettes

Author: mhurtado13

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# 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:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+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@v4
+
+      - 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@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 inst/doc
+docs

DESCRIPTION

@@ -67,3 +67,4 @@ LazyData: true
 LazyDataCompression: bzip2
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+URL: https://mhurtado13.github.io/multideconv/

R/cell_deconvolution.R

@@ -8,7 +8,6 @@ if (!dir.exists(signature_dir)) {
   dir.create(signature_dir, recursive = TRUE)
 }
 
-library(pcaMethods) #Explicitly loading pcaMethods to access functions like prep(), which are not imported via @import. Problem with DeconRNASeq that uses not imported functions from pcaMethods
 utils::globalVariables(c("mcp", "xcell" ,"i", ".", "samples_ids", "multisession", ".data", "Patient", "var", "id", "value", "P", "sig_p", "r", "y", "p", "average", "Cells", "variable", "value", "pval_value"))
 
 #' Compute deconvolution preprocessing
@@ -1389,6 +1388,7 @@ computeEpiDISH = function(TPM_matrix, signature_file, name_signature){
 #'
 #' @import pcaMethods
 computeDeconRNASeq = function(TPM_matrix, signature_file, name_signature){
+  library(pcaMethods) #Explicitly loading pcaMethods to access functions like prep(), which are not imported via @import. Problem with DeconRNASeq that uses not imported functions from pcaMethods
 
   decon <- DeconRNASeq::DeconRNASeq(TPM_matrix, data.frame(signature_file))
   deconRNAseq = decon$out.all
@@ -1599,10 +1599,8 @@ compute_methods_variable_signature = function(TPM_matrix, signatures, algos = c(
 #' data("pseudobulk")
 #'
 #' deconv = compute.deconvolution(raw_counts, normalized = TRUE,
-#'                                methods = c("DWLS", "DeconRNASeq"), return = FALSE)
+#'                                methods = c("Epidish", "DeconRNASeq"), return = FALSE)
 #'
-#' deconv = compute.deconvolution(raw_counts, normalized = TRUE, methods = "DWLS",
-#'                                signatures_exclude = "BPRNACan", return = FALSE)
 #'
 #' @references
 #'

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://mhurtado13.github.io/multideconv/
+template:
+  bootstrap: 5
+

man/compute.deconvolution.Rd

@@ -0,0 +1,2 @@
+*.html
+*.R