Merge branch 'development' of github.com:saezlab/MetaProViz into deve…

…lopment
saezlab · Oct 28, 2024 · d33f868 · d33f868
2 parents 2f0ef89 + 0542660
commit d33f868
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -0,0 +1,7 @@
+[bumpversion]
+current_version = 2.1.1
+commit = True
+tag = True
+files = DESCRIPTION README.md README.Rmd
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
+serialize = {major}.{minor}.{patch}
diff --git a/.github/workflows/Build_gh-pages.yml b/.github/workflows/Build_gh-pages.yml
@@ -0,0 +1,38 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples and adapted
+on:
+  push:
+    branches: [main]
+
+name: Build_gh-pages.yml #shown when action is run
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    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/
+      - uses: actions/checkout@v4 # goes to gh-pages branch to work there
+
+      - uses: r-lib/actions/setup-pandoc@v2 #installs pandoc
+
+      - uses: r-lib/actions/setup-r@v2 #installs R
+        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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/Test_Package-build.yml b/.github/workflows/Test_Package-build.yml
@@ -0,0 +1,47 @@
+# 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
+# This workflow tests if the package can be installed from github from within
+# a github action.
+on:
+  push:
+    branches: [development, main]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install libglpk40
+        if: ${{ matrix.config.os == 'ubuntu-latest' }}
+        run: sudo apt-get install -y libglpk40
+
+      - 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
+
+      - name: Install pak
+        run: Rscript -e 'install.packages("pak")'
+
+      - name: Install MetaProViz from git by pak
+        run: Rscript -e 'pak::pkg_install("saezlab/MetaProViz")' #we install from GitHub as if we are a random user
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MetaProViz
 Title: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
-Version: 2.1.0
+Version: 2.1.1
 Authors@R: c(
     person("Christina", "Schmidt", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3867-0881")),
@@ -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,

diff --git a/R/Processing.R b/R/Processing.R
diff --git a/R/VizHeatmap.R b/R/VizHeatmap.R
@@ -179,6 +179,7 @@ VizHeatmap <- function(InputData,
       # Make the plot
       if(nrow(t(data_path))>= 2){
         set.seed(1234)
+
         heatmap <- pheatmap::pheatmap(t(data_path),
                                      show_rownames = as.logical(show_rownames),
                                      show_colnames = as.logical(show_colnames),
@@ -193,16 +194,17 @@ VizHeatmap <- function(InputData,
                                      fontsize_row= 10,
                                      fontsize_col = 10,
                                      fontsize=9,
-                                     main = paste(PlotName, " Metabolites: ", i, sep=" " ))
+                                     main = paste(PlotName, " Metabolites: ", i, sep=" " ),
+                                     silent = TRUE)
 
         ## Store the plot in the 'plots' list
         cleaned_i <- gsub("[[:space:],/\\\\]", "-", i)#removes empty spaces and replaces /,\ with -
         PlotList[[cleaned_i]] <- heatmap
 
         #Width and height according to Sample and metabolite number
-        Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, PlotName= cleaned_i)
-        PlotHeight <- as.numeric(Plot_Sized$height)
-        PlotWidth <- as.numeric(Plot_Sized$width)
+        Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample, SettingsFile_Metab=SettingsFile_Metab, PlotName= cleaned_i)
+        PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+        PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
         Plot_Sized %<>%
           {ggplot2::ggplot() + annotation_custom(.)} %>%
           add(theme(panel.background = element_rect(fill = "transparent")))
@@ -316,6 +318,7 @@ VizHeatmap <- function(InputData,
         # Make the plot
         if(nrow(t(data_path))>= 2){
         set.seed(1234)
+
         heatmap <- pheatmap::pheatmap(t(data_path),
                                       show_rownames = as.logical(show_rownames),
                                       show_colnames = as.logical(show_colnames),
@@ -330,16 +333,17 @@ VizHeatmap <- function(InputData,
                                       fontsize_row= 10,
                                       fontsize_col = 10,
                                       fontsize=9,
-                                      main = paste(PlotName," Samples: ", i, sep=" " ))
+                                      main = paste(PlotName," Samples: ", i, sep=" " ),
+                                      silent = TRUE)
 
         #----- Save
         cleaned_i <- gsub("[[:space:],/\\\\]", "-", i)#removes empty spaces and replaces /,\ with -
         PlotList[[cleaned_i]] <- heatmap
 
         #Width and height according to Sample and metabolite number
-        Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, PlotName= cleaned_i)
-        PlotHeight <- as.numeric(Plot_Sized$height)
-        PlotWidth <- as.numeric(Plot_Sized$width)
+        Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample, SettingsFile_Metab=SettingsFile_Metab, PlotName= cleaned_i)
+        PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+        PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
         Plot_Sized %<>%
           {ggplot2::ggplot() + annotation_custom(.)} %>%
           add(theme(panel.background = element_rect(fill = "transparent")))
@@ -474,6 +478,7 @@ VizHeatmap <- function(InputData,
             # Make the plot
             if(nrow(t(data_path))>= 2){
             set.seed(1234)
+
             heatmap <- pheatmap::pheatmap(t(data_path),
                                           show_rownames = as.logical(show_rownames),
                                           show_colnames = as.logical(show_colnames),
@@ -488,7 +493,8 @@ VizHeatmap <- function(InputData,
                                           fontsize_row= 10,
                                           fontsize_col = 10,
                                           fontsize=9,
-                                          main = paste(PlotName," Metabolites: ", i, " Sample:", s, sep="" ))
+                                          main = paste(PlotName," Metabolites: ", i, " Sample:", s, sep="" ),
+                                          silent = TRUE)
 
             ## Store the plot in the 'plots' list
             cleaned_i <- gsub("[[:space:],/\\\\]", "-", i)#removes empty spaces and replaces /,\ with -
@@ -498,9 +504,9 @@ VizHeatmap <- function(InputData,
             #-------- Plot width and heights
             #Width and height according to Sample and metabolite number
             PlotName <- paste(cleaned_i,cleaned_s, sep="_")
-            Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, PlotName= PlotName)
-            PlotHeight <- as.numeric(Plot_Sized$height)
-            PlotWidth <- as.numeric(Plot_Sized$width)
+            Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample, SettingsFile_Metab=SettingsFile_Metab, PlotName= PlotName)
+            PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+            PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
             Plot_Sized %<>%
               {ggplot2::ggplot() + annotation_custom(.)} %>%
               add(theme(panel.background = element_rect(fill = "transparent")))
@@ -589,6 +595,7 @@ VizHeatmap <- function(InputData,
     #Make the plot:
     if(nrow(t(data))>= 2){
     set.seed(1234)
+
     heatmap <- pheatmap::pheatmap(t(data),
                                   show_rownames = as.logical(show_rownames),
                                   show_colnames = as.logical(show_colnames),
@@ -603,16 +610,17 @@ VizHeatmap <- function(InputData,
                                   fontsize_row= 10,
                                   fontsize_col = 10,
                                   fontsize=9,
-                                  main = PlotName)
+                                  main = PlotName,
+                                  silent = TRUE)
 
     ## Store the plot in the 'plots' list
     PlotList[[PlotName]] <- heatmap
 
     #-------- Plot width and heights
     #Width and height according to Sample and metabolite number
-    Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, PlotName= PlotName)
-    PlotHeight <- as.numeric(Plot_Sized$height)
-    PlotWidth <- as.numeric(Plot_Sized$width)
+    Plot_Sized <- PlotGrob_Heatmap(InputPlot=heatmap, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample, SettingsFile_Metab=SettingsFile_Metab, PlotName= PlotName)
+    PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+    PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
     Plot_Sized %<>%
       {ggplot2::ggplot() + annotation_custom(.)} %>%
       add(theme(panel.background = element_rect(fill = "transparent")))
@@ -630,7 +638,7 @@ VizHeatmap <- function(InputData,
                            CoRe=FALSE,
                            PrintPlot=PrintPlot,
                            PlotHeight=PlotHeight,
-                           PlotWidth=PlotHeight,
+                           PlotWidth=PlotWidth,
                            PlotUnit="cm")))
 
 
@@ -649,12 +657,14 @@ VizHeatmap <- function(InputData,
 
 #' @param InputPlot This is the ggplot object generated within the VizHeatmap function.
 #' @param SettingsInfo Passed to VizHeatmap
+#' @param SettingsFile_Sample Passed to VizHeatmap
+#' @param SettingsFile_Metab Passed to VizHeatmap
 #' @param PlotName Passed to VizHeatmap
 #'
 #' @keywords Heatmap helper function
 #' @noRd
 
-PlotGrob_Heatmap <- function(InputPlot, SettingsInfo, PlotName){
+PlotGrob_Heatmap <- function(InputPlot, SettingsInfo, SettingsFile_Sample, SettingsFile_Metab, PlotName){
 
   # Set the parameters for the plot we would like to use as a basis, before we start adjusting it:
   HEAT_PARAM <- list(
@@ -666,19 +676,71 @@ PlotGrob_Heatmap <- function(InputPlot, SettingsInfo, PlotName){
     )
   )
 
+  #If we plot feature names on the x-axis, we need to adjust the height of the plot:
+  #if(as.logical(show_rownames)==TRUE){
+  #  Rows <- nrow(t(data))
+  #}
 
   #Adjust the parameters:
   Input <- InputPlot$gtable
 
   Plot_Sized <- Input  %>%
     withCanvasSize(width = 12, height = 11) %>%
-    adjust_layout(HEAT_PARAM) #%>%
-    #adjust_title(c(PlotName)) %>%
-    #adjust_legend(
-    #  Input,
-    #  sections = c("color_Sample", "color_Metab"),#How can we do this as here we have multiple once!
-    #  SettingsInfo = SettingsInfo
-    #)
+    adjust_layout(HEAT_PARAM) %>%
+    adjust_title(c(PlotName))
+
+  #Extract legend information and adjust:
+  color_entries <- grep("^color", names(SettingsInfo), value = TRUE)
+  if(length(color_entries)>0){#We need to adapt the plot Hights and widths
+    if(sum(grepl("color_Sample", names(SettingsInfo)))>0){
+      names <- SettingsInfo[grepl("color_Sample", names(SettingsInfo))]
+      colour_names <- NULL
+      legend_names <- NULL
+      for (x in 1:length(names)){
+        names_sel <- names[[x]]
+        legend_names[x] <- names_sel
+        colour_names[x] <- SettingsFile_Sample[names[[x]]]
+      }
+    }else{
+      colour_names <- NULL
+      legend_names <- NULL
+    }
+
+    if(sum(grepl("color_Metab", names(SettingsInfo)))>0){
+      names <- SettingsInfo[grepl("color_Metab", names(SettingsInfo))]
+      colour_names_M <- NULL
+      legend_names_M <- NULL
+      for (x in 1:length(names)){
+        names_sel <- names[[x]]
+        legend_names_M[x] <- names_sel
+        colour_names_M[x] <- SettingsFile_Metab[names[[x]]]
+      }
+    }else{
+      colour_names_M <- NULL
+      legend_names_M <- NULL
+    }
+
+    legend_head <- c(legend_names, legend_names_M)
+    longest_name <- legend_head[which.max(nchar(legend_head[[1]]))]
+    character_count_head <- nchar(longest_name)+4#This is the length of the legend title name
+
+    legend_names <- c(unlist(colour_names), unlist(colour_names_M))
+    longest_name <- legend_names[which.max(nchar(legend_names[[1]]))]
+    character_count <- nchar(longest_name)#This is the length of the legend colour names
+
+    legendWidth <-  unit(((max(character_count_head, character_count))*0.3), "cm")#legend space
+
+    # Sum up total heights:
+    Plot_Sized$width %<>% add(legendWidth)
+
+    legendHeights <- unit((sum(length(unique(legend_names_M))+length(unique(colour_names_M))+length(unique(legend_names))+length(unique(colour_names)))), "cm")
+
+    Plot_Sized$width %<>% add(legendWidth)
+    if((grid::convertUnit(legendHeights, 'cm', valueOnly = TRUE))>(grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE))){
+      Plot_Sized$height <- legendHeights
+    }
+
+  }
 
   Output <- Plot_Sized
 

diff --git a/R/VizSuperplots.R b/R/VizSuperplots.R
@@ -358,8 +358,8 @@ VizSuperplot <- function(InputData,
 
     # Make plot into nice format:
     Plot_Sized <-  MetaProViz:::plotGrob_Superplot(InputPlot=Plot, SettingsInfo=SettingsInfo, SettingsFile_Sample=SettingsFile_Sample,  PlotName = PlotName, Subtitle = i, PlotType=PlotType)
-    PlotHeight <- as.numeric(Plot_Sized$height)
-    PlotWidth <- as.numeric(Plot_Sized$width)
+    PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+    PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
     Plot_Sized %<>%
       {ggplot2::ggplot() + annotation_custom(.)} %>%
       add(theme(panel.background = element_rect(fill = "transparent")))
@@ -412,7 +412,7 @@ plotGrob_Superplot <- function(InputPlot,
                                PlotType){
   # Set the parameters for the plot we would like to use as a basis, before we start adjusting it:
   X_Con <- SettingsFile_Sample%>%
-    dplyr::distinct(!!sym(SettingsInfo[["Conditions"]]))
+    dplyr::distinct(Conditions)
 
   X_Tick <- unit(X_Con[[1]] %>% char2cm %>% max * 0.6, "cm")
 

diff --git a/R/VizVolcano.R b/R/VizVolcano.R
@@ -562,8 +562,8 @@ VizVolcano_Standard <- function(InputData,
 
       #Set the total heights and widths
       Plot_Sized <-  MetaProViz:::plotGrob_Volcano(InputPlot=Plot, SettingsInfo=SettingsInfo,  PlotName = PlotName, Subtitle = Subtitle)
-      PlotHeight <- as.numeric(Plot_Sized$height)
-      PlotWidth <- as.numeric(Plot_Sized$width)
+      PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+      PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
       Plot_Sized %<>%
         {ggplot2::ggplot() + annotation_custom(.)} %>%
         add(theme(panel.background = element_rect(fill = "transparent")))
@@ -926,8 +926,8 @@ VizVolcano_Compare <- function(InputData,
       PlotList[["Plot"]] <- Plot
 
       Plot_Sized <-  MetaProViz:::plotGrob_Volcano(InputPlot=Plot, SettingsInfo=SettingsInfo,  PlotName = PlotName, Subtitle = Subtitle)
-      PlotHeight <- as.numeric(Plot_Sized$height)
-      PlotWidth <- as.numeric(Plot_Sized$width)
+      PlotHeight <- grid::convertUnit(Plot_Sized$height, 'cm', valueOnly = TRUE)
+      PlotWidth <- grid::convertUnit(Plot_Sized$width, 'cm', valueOnly = TRUE)
       Plot_Sized %<>%
         {ggplot2::ggplot() + annotation_custom(.)} %>%
         add(theme(panel.background = element_rect(fill = "transparent")))