Build fix: remove R packages not utilized, remove unnecessary files i…

…n Docker build (#571)

.github/workflows/biocbook.yml

@@ -15,7 +15,6 @@ jobs:
       packages: write
 
     steps:
-
       - name: 🧾 Checkout repository
         uses: actions/checkout@v3
 
@@ -26,12 +25,20 @@ jobs:
         run: |
           docker system prune --all --force --volumes
 
+      - name: 🧹 Additional disk space cleanup
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf /usr/local/lib/android/sdk
+          sudo apt-get clean
+          sudo rm -rf /var/lib/apt/lists/*
+
       - name: 🐳 Set up QEMU
         uses: docker/setup-qemu-action@v2
 
       - name: 🐳 Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
-  
+
       - name: 📦 Cache Docker layers
         uses: actions/cache@v3
         with:
@@ -81,7 +88,7 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           build-args: |
             BIOC_VERSION=${{ github.ref_name }}
-    
+
       - name: 🚀 Push local Docker image to ghcr.io
         uses: docker/build-push-action@v4
         with:
@@ -93,7 +100,7 @@ jobs:
           build-args: |
             BIOC_VERSION=${{ github.ref_name }}
 
-      - name: 📚 Recover pkg artifacts generated during build in local Docker container (pkg bundle and book) 
+      - name: 📚 Recover pkg artifacts generated during build in local Docker container (pkg bundle and book)
         env:
           IMG: ${{ steps.docker.outputs.ImageID }}
         run: |
@@ -110,10 +117,10 @@ jobs:
       - name: 🚀 Deploy book to Github Pages on versioned branch
         uses: JamesIves/[email protected]
         with:
-          folder: ${{ env.book_path }}/ 
-          target-folder: docs/${{ env.target_folder }}/ 
+          folder: ${{ env.book_path }}/
+          target-folder: docs/${{ env.target_folder }}/
           branch: gh-pages
-          clean: false 
+          clean: false
 
       - name: 💾 Upload package bundle artifact
         uses: actions/upload-artifact@v3
@@ -125,4 +132,4 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: book
-          path: ${{ env.book_path }}
+          path: ${{ env.book_path }}

DESCRIPTION

@@ -28,73 +28,71 @@ Depends:
     R (>= 4.0.0)
 Imports:
 Suggests:
-    ALDEx2, 
-    ANCOMBC, 
-    ape, 
-    biclust, 
+    ALDEx2,
+    ANCOMBC,
+    ape,
+    biclust,
     BiocBook,
     BiocManager,
     BiocParallel,
-    Biostrings,     
-    bluster, 
+    Biostrings,
+    bluster,
     caret,
-    circlize, 
+    circlize,
     cluster,
-    cobiclust, 
-    ComplexHeatmap, 
+    cobiclust,
+    ComplexHeatmap,
     corpcor,
-    cowplot, 
-    curatedMetagenomicData, 
+    curatedMetagenomicData,
     dada2,
-    dendextend, 
+    dendextend,
     devtools,
     DirichletMultinomial,
-    dplyr,    
+    dplyr,
     DT,
     factoextra,
     forcats,
     fido,
-    ggplot2, 
+    ggplot2,
     ggpubr,
     ggtree,
-    glmnet,    
-    glue, 
+    glmnet,
+    glue,
     grid,
     gsEasy,
-    gtools,
-    GUniFrac,
-    igraph, 
-    kableExtra, 
-    knitr, 
+    igraph,
+    kableExtra,
+    knitr,
     Maaslin2,
     mia,
     miaTime,
-    miaViz, 
-    microbiome, 
+    miaViz,
+    microbiome,
     microbiomeDataSets,
     MicrobiomeStat,
-    mikropml,    
-    MLeval,
+    mikropml,
     MMUPHin,
+    MOFA2,
     multiview,
     NetCoMi,
     NbClust,
+    NMF,
     patchwork,
-    pheatmap, 
-    phyloseq, 
-    plotly, 
-    purrr, 
-    randomcoloR,
+    phyloseq,
+    plotly,
+    purrr,
+    qgraph,
     RColorBrewer,
     rebook,
     reshape2,
     reticulate,
     rgl,
-    ROCR,    
+    ROCR,
     scales,
-    scater, 
-    sechm, 
+    scater,
+    sechm,
     sessioninfo,
+    shadowtext,
     SpiecEasi,
     SPRING,
     stats,
@@ -104,11 +102,6 @@ Suggests:
     topGO,
     vegan,
     WGCNA,
-    NMF,
-    qgraph,
-    MOFA2,
-    shadowtext,
-    plotROC,
     xgboost
 Remotes:
     github::microbiome/mia,

inst/pages/exercises.qmd

@@ -1392,8 +1392,6 @@ named `tse`.
 #| code-summary: "Show solution"
 
 library(mia)
-library(GUniFrac)
-
 data("peerj13075", package = "mia")
 tse <- peerj13075
 ```
@@ -1484,7 +1482,7 @@ whether the difference of certain taxa was statistically significant.
 boxplot & jitterplot.
 
 Useful functions: wilcox.test, kruskal.test, ggplot2::ggplot,
-pheatmap::pheatmap, ComplexHeatMap::Heatmap, ANCOMBC::ancombc2,
+ComplexHeatmap::pheatmap, ComplexHeatMap::Heatmap, ANCOMBC::ancombc2,
 ALDEx2::aldex, Maaslin2::Maaslin2, agglomerateByRank, transformAssay,
 subsetByPrevalent
 
@@ -1719,7 +1717,7 @@ sample types).
 ```{r, eval = FALSE}
 # Load necessary libraries
 library(SummarizedExperiment)
-library(pheatmap)
+library(ComplexHeatmap)
 
 # Example data creation
 # Assuming enterotype is a SummarizedExperiment object with sample metadata

inst/pages/extra_material.qmd

@@ -742,7 +742,7 @@ clusters$classification
 Next we can plot clusters. Annotated heatmap is a common choice.
 
 ```{r cobiclust_3a, fig.width=14, fig.height=12}
-library(pheatmap)
+library(ComplexHeatmap)
 # z-transform for heatmap
 mae[[1]] <- transformAssay(
     mae[[1]], assay.type = "rclr", MARGIN = "features", method = "z",

inst/pages/extra_material/24_biclustering.Rmd

@@ -76,7 +76,7 @@ Next we can plot clusters. Commonly used plot is heatmap with annotations.
 
 ```{r cobiclust_3, fig.width=14, fig.height=18}
 
-library(pheatmap)
+library(ComplexHeatmap)
 
 # standardize-transform for heatmap
 mae[[1]] <- transformAssay(mae[[1]], assay.type = "rclr",

inst/pages/extra_material/add-comm-typing.Rmd

@@ -160,7 +160,7 @@ The community composition can be visualised with a heatmap where one axis repres
 Here, the CLR + Z-transformed abundances are shown.
 
 ```{r, message=FALSE, warning=FALSE}
-library(pheatmap)
+library(ComplexHeatmap)
 library(grid)
 library(RColorBrewer)
 # Agglomerate to phylum level

inst/pages/machine_learning.qmd

@@ -211,21 +211,14 @@ technique for binary classification problems.
 ```{r}
 #| label: ROC
 
-library(plotROC)
-
-# Add observation as binary
-res[["obs_binary"]] <- 0
-res[["obs_binary"]][ res[["obs"]] == "healthy" ] <- 1
-roc_plot <- ggplot(res, aes(m = .data[["healthy"]], d = .data[["obs_binary"]])) + 
-    geom_roc(labels = FALSE, n.cuts = 0) +
-    labs(x = "False Positive Rate", y = "True Positive Rate")
-# Add AUC
-p <- roc_plot +
-    geom_rocci(fill="pink", sig.level = 0.05) +
-    geom_text(aes(
-        0.5, 0.5, label = paste0("AUC = ", round(calc_auc(roc_plot)$AUC, 3))
-        )) +
-    theme(legend.position="none")
+library(ROCR)
+
+# Get positive class
+pos_class <-levels(res[["obs"]])[[1]]
+# Create ROC plot
+pred <- prediction(res[[pos_class]], ifelse(res[["obs"]] == pos_class, 1, 0))
+perf <- performance(pred, measure = "tpr", x.measure = "fpr")
+p <- plot(perf)
 p
 ```
 

inst/pages/visualization.qmd

@@ -31,7 +31,7 @@ includes the following packages:
 * _patchwork_, _cowplot_, _ggpubr_ and _gridExtra_: plot layouts and multi-panel plotting
 * _miaViz_: specific visualization tools for `TreeSummaizedExperiment` objects
 * _scater_: specific visualization tools for `SingleCellExperiment` objects
-* _ggplot2_, _pheatmap_, _ggtree_, _sechm_: composition heatmaps
+* _ggplot2_, _ComplexHeatmap_, _ggtree_, _sechm_: composition heatmaps
 * _ANCOMBC_, _ALDEx2_ and _Maaslin2_: visual differential abundance
 * _fido_: tree-based methods for differential abundance
 * _plotly_: animated and 3D plotting
@@ -51,7 +51,7 @@ library(patchwork)
 library(miaViz)
 library(sechm)
 library(reshape2)
-library(pheatmap)
+library(ComplexHeatmap)
 library(ape)
 library(ggtree)
 # essential data