Merge pull request #85 from saezlab/main

Main has github action required changed

.github/workflows/Build_gh-pages.yml

@@ -1,17 +1,17 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples and adapted
 on:
   push:
-    branches: [main, master]
+    branches: [main]
 
 name: Build_gh-pages.yml #shown when action is run
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-   env:
+    env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} #to push results to gh-pages branch!
-   steps: #Series of steps that is executed sequencially: https://github.com/r-lib/actions/
+    steps: #Series of steps that is executed sequencially: https://github.com/r-lib/actions/
       - uses: actions/checkout@v4 # goes to gh-pages branch to work there
 
       - uses: r-lib/actions/setup-pandoc@v2 #installs pandoc
@@ -22,11 +22,17 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown
+          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 🚀
-        run: |
-          git config --local user.name "GitHub Actions"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -31,16 +31,24 @@ Depends:
     R (>= 4.4.1),
     ggplot2 (>= 3.3.5)
 Imports:
+    clusterProfiler,
+    cosmosR,
     dplyr,
+    EnhancedVolcano,
     factoextra,
+    ggbeeswarm,
     ggfortify,
     ggplot2,
     ggupset,
+    ggVennDiagram,
     grid,
     gridExtra,
     gtools,
     hash,
     inflection,
+    kableExtra,
+    KEGGREST,
+    limma,
     logger,
     magrittr,
     OmnipathR,

R/Processing.R

@@ -482,7 +482,7 @@ PoolEstimation <- function(InputData,
                         labs(title="CV for metabolites of Pool samples",x="Coefficient of variation (CV%)", y = "Frequency")+
                         theme_classic()))
 
-  HistCV_Sized <- MetaProViz:::plotGrob_Processing(InputPlot =  HistCV, PlotName= "CV for metabolites of Pool samples", , PlotType= "Hist")
+  HistCV_Sized <- MetaProViz:::plotGrob_Processing(InputPlot =  HistCV, PlotName= "CV for metabolites of Pool samples", PlotType= "Hist")
   PlotList [["Histogram_CV-PoolSamples"]] <- HistCV_Sized
 
   # 2. ViolinPlot of CVs
@@ -503,7 +503,7 @@ PoolEstimation <- function(InputData,
                           labs(title="CV for metabolites of Pool samples",x="Metabolites", y = "Coefficient of variation (CV%)")+
                           theme_classic())
 
-  ViolinCV_Sized <- MetaProViz:::plotGrob_Processing(InputPlot = ViolinCV, PlotName= "CV for metabolites of Pool samples", , PlotType= "Violin")
+  ViolinCV_Sized <- MetaProViz:::plotGrob_Processing(InputPlot = ViolinCV, PlotName= "CV for metabolites of Pool samples", PlotType= "Violin")
 
   PlotList [["ViolinPlot_CV-PoolSamples"]] <- ViolinCV_Sized
 
@@ -883,8 +883,8 @@ TICNorm <-function(InputData, SettingsFile_Sample, TIC){
 
     #Combine Plots
     dev.new()
-    norm_plots <- suppressWarnings(gridExtra::grid.arrange(RLA_data_raw_Sized+ theme(axis.text.x = element_text(angle = 90, hjust = 1))+ theme(legend.position = "none"),
-                                                           RLA_data_norm_Sized+ theme(axis.text.x = element_text(angle = 90, hjust = 1))+ theme(legend.position = "none"),
+    norm_plots <- suppressWarnings(gridExtra::grid.arrange(RLA_data_raw+ theme(axis.text.x = element_text(angle = 90, hjust = 1))+ theme(legend.position = "none"),
+                                                           RLA_data_norm+ theme(axis.text.x = element_text(angle = 90, hjust = 1))+ theme(legend.position = "none"),
                                                            ncol = 2))
     dev.off()
     norm_plots <- ggplot2::ggplot() +theme_minimal()+ annotation_custom(norm_plots)