How to modify the plot sizes in shiny app?

Question

I built a shiny app which present several plot types. However, the plots are cut from the top, and they are too wide. I tried modifying the width and height in the plotOutput function, did not work.

My code:

ui <- fluidPage(theme = shinytheme('united'),
  titlePanel(title = h3("Graphs - ordered chronologically", align="center")),
  selectInput("Plot", 
              "Choose what plots to present", 
              choices = list(Heatmap = "Heatmap", PCA = "PCA", VolcanoPlot = "VolcanoPlot", GSEA = 'GSEA')),
  submitButton(text = "Show plots"),
  verticalLayout( plotOutput(outputId = "PART.1", width = '70%'))
)

The problem is most prominent with the Heatmaps and Volcano plots. The volcano plot is cut from the top, and the heatmaps are too stretched wide:

How can I fix this? thank you.

EDIT:

A minimal version of my code:

    library(data.table)
    library(dplyr)
    library(shiny)
    library(shinythemes)
    library(plotly)
    library(compGenomRData)
    library(BiocManager)
    library(DESeq2)
    library(org.Hs.eg.db)
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(EnsDb.Hsapiens.v86)
    library(AnnotationHub)
    library(AnnotationDbi)
    library(pheatmap)
    library(EnhancedVolcano)
    library(ggplot2)
    library(FactoMineR)
    library(devtools)
    library(clusterProfiler)
    library(ggnewscale)
    library(enrichplot)
    library(msigdbr)
    library(readxl)
      library(ExperimentHub)
    library(annotate)

    ui <- fluidPage(theme = shinytheme('united'),
      titlePanel(title = h3("Graphs - ordered chronologically", align="center")),
      selectInput("Plot", 
                  "Choose which plots to present", 
                  choices = list(Heatmap = "Heatmap", PCA = "PCA", VolcanoPlot = "VolcanoPlot", GSEA = 'GSEA')),
      submitButton(text = "Show plots"),
      verticalLayout( plotOutput(outputId = "PART.1", width = '70%'),
      plotOutput(outputId = "PART.2", width = '70%'),
      plotOutput(outputId = "PART.3", width = '70%'),
      plotOutput(outputId = "PART.4", width = '70%'),
      plotOutput(outputId = "PART.5", width = '70%'),
      plotOutput(outputId = "PART.6", width = '70%'),
      plotOutput(outputId = "PART.7", width = '70%'))
    )
    
    server <- function(input, output) {


      # RNA-seq data
      raw_counts <- frea
    d('E-MTAB-7805-raw-counts.tsv', data.table = F) 
      metadata <- fread('E-MTAB-7805-experiment-design.tsv' ,data.table = F)
      
      
      A=duplicated(raw_counts$`Gene ID`) # Check for duplicates and remove them
      raw_counts = raw_counts[!A,]
      A=duplicated(raw_counts$`Gene Name`) # Check for duplicates and remove them
      raw_counts = raw_counts[!A,]
  
      
      Hugo.Symbol <- raw_counts[,c(1:2)]
      rownames(raw_counts) <- raw_counts$`Gene Name` # renaming rownames
      raw_counts <- raw_counts[, -c(1:2)]
      
      # metadata
      C = duplicated(metadata$Run) # Check for duplicates and remove them
      metadata = metadata[!C,]
      
      rownames(metadata) <- metadata$Run
      metadata <- metadata[,-1]
      
      ind <- order(colnames(raw_counts), rownames(metadata))
      raw_counts <- raw_counts[,ind]

       
  # filter
  target1 <- c("0 day", "1 day")
  Meta_filter1 <- metadata %>% dplyr::filter(`Factor Value[time]` %in%  target1)
  Counts_filter1 <- raw_counts[intersect(names(raw_counts), rownames(Meta_filter1))]
  rownames(Counts_filter1) <- Hugo.Symbol$`Gene Name`
  
  
  
  # annotate
  Meta_filter1$group <- plyr::mapvalues(Meta_filter1$`Factor Value[time]`, c("0 day", "1 day"),
                                        c("CTRL", "CASE"))
  ind <- order(colnames(Counts_filter1), rownames(Meta_filter1))
  Counts_filter1 <- Counts_filter1[,ind]


      dds <- DESeqDataSetFromMatrix(countData =  Counts_filter1,
                                     colData =  Meta_filter1,
                                     design = ~ group)
      
      dds = DESeq(dds)
      
      res = results(dds)
      res$symbol <- rownames(res)
      resOrder <- res[order(res$padj),]
      
      
      # heatmap
      dds.symbol = dds
      rownames(dds.symbol) = mapIds(org.Hs.eg.db,
                                    keys=rownames(dds),
                                    column="SYMBOL",
                                    keytype="SYMBOL",
                                    multiVals="first")
      rownames(dds.symbol)[is.na(rownames(dds.symbol))] = rownames(dds)[is.na(rownames(dds.symbol))]
      rownames(dds.symbol) = make.unique(rownames(dds.symbol))
      
      selectUp <- resOrder$symbol[resOrder$log2FoldChange>0][1:20]
      selectDown <- resOrder$symbol[resOrder$log2FoldChange<0][1:20]
      select = c(selectUp,selectDown)
      df <- data.frame(row.names = colnames(dds.symbol),
                       group = colData(dds.symbol)$group)
      
      normcounts = assay(vst(dds.symbol,blind=T, nsub = 2000))
      
      
      # Functional enrichment
      res = res[!is.na(res1$padj),]
      mygenes <- rownames(res)
      
      lfc = res1$log2FoldChange # get gene symbol
      names(lfc) <- rownames(res) 
      lfc <- sort(lfc, decreasing = TRUE)
      
      hallmarks <- msigdbr(species = "Homo sapiens", category = "H") %>% 
        dplyr::select(gs_name, gene_symbol)
    
    ## Output 
      
      output$PART.1 <- renderPlot({
        if (input$Plot == 'Heatmap') { 
          
          pheatmap(normcounts[select,], cluster_rows=TRUE,
                         show_colnames = FALSE,cluster_cols=TRUE, 
                         annotation_col=df, scale = 'row',cutree_cols = 2,cutree_rows = 2)
          
          
          
        } else if (input$Plot == 'PCA') {
          Var <- apply(normcounts, 1, var)
          selectedVarGenes <- names(Var[order(Var, decreasing = T)][1:1000])
          M <- t(normcounts[selectedVarGenes,])
          pcaResults = prcomp(M)
          qplot(pcaResults$x[,1],pcaResults$x[,2], col=dds1$group,size=2)
    
          
          
        } else if (input$Plot == 'VolcanoPlot') {
          
    
          EnhancedVolcano(resOrder,
                          lab = resOrder$symbol,
                          x = 'log2FoldChange',
                          y = 'padj',
                          labSize=4,
                          FCcutoff=2 )
     
          
          
        } else  {
          em <- GSEA(lfc, TERM2GENE = hallmarks)
          dotplot(em)
          
          
        }
        
      })
      
    shinyApp(ui = ui, server = server)

How to modify the plot sizes in shiny app?

My code:

EDIT:

Answers (1)

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