inst/shiny/modules/13-ui-gProfiler.R

In goushixue/QRseq: Quickly RNA-seq Analysis Platform

fluidPage(
  style = "margin-left: 10px; margin-right:10px;",
  box(
    title = "Runing gProfiler:", id = "gprofiler_tab", width = 12, collapsible = TRUE, solidHeader = TRUE,
    fluidRow(
      column(3, style = "height:74px", selectInput("gprofiler_genes", "What genes to used:",  c("DEGs", "DEG Patterns", "WGCNA Modules"),width = "100%")),
      column(3, style = "height:74px", uiOutput('gprofiler_gsets')),
      column(3, style = "height:74px", numericInput("gprofiler_pval", "Pvalue threshold:", value = 0.05,  min = 0, max = 1, width = "100%")),
      column(3, style = "height:74px", selectInput("gprofiler_cor_method", "Correction method:",
                            c("g_SCS", "bonferroni", "fdr", "false_discovery_rate", "gSCS","analytical"), width = "100%")),
      column(3, style = "height:74px", selectInput("gprofiler_evcodes", "Show evidence:", c("TRUE", "FALSE"), width = "100%")),
      column(
        3, style = "height:74px",
        virtualSelectInput(
          inputId = "gprofiler_sources",  label = "Data sources to use::", 
          choices = c("GO:BP", "GO:MF", "GO:CC", "KEGG", "REAC", "TF", "MIRNA", "CORUM", "HP", "HPA", "WP"),
          selected = c("GO:BP", "GO:MF", "GO:CC", "KEGG", "REAC"),  multiple = T, search = F, width = "100%"
        )
      ),
      column(3, style = "height:74px", selectInput("gprofiler_significant", "Only return significant results:", choices = c("TRUE", "FALSE"), width = "100%")),
      column(3, style = "height:74px", selectInput("gprofiler_excludeIEA", "Exclude GO electronic annotations:", choices = c("FALSE","TRUE"), width = "100%")),
      column( 12, align = "center", actionButton("runGprofiler", "Run gProfiler", class = "run-button", width = "30%") )
    )
  ),
  column(
    12,
    conditionalPanel(
      "input.runGprofiler",
      tabsetPanel(
        tabPanel(
          "Enrichment Results Visualization",
          fluidPage(
            style = "padding-top: 5px; padding-left: 0px; padding-right: 0px;margin-left: 0px; margin-right: 0px;",
            box(
              title = "Enrichment Results Visualiztion", width = 4, collapsible = T, solidHeader = TRUE,
              uiOutput("gprofiler_plot_type"),
              uiOutput("sourceTypes"),
              conditionalPanel(
                "input.gprofiler_type=='dotplot'",
                selectInput("gprofiler_orderBy", "Order results by:", c("precision", "recall"), width = "100%"),
                selectInput("gprofiler_Top", "Auto or custom choices terms:", c("use topN terms", "custom select terms"), width = "100%"),
                conditionalPanel(
                  "input.gprofiler_Top=='use topN terms'",
                  numericInput("gprofiler_n_terms", "TopN terms:", value = 20, width = "100%")
                )
              ),
              conditionalPanel(
                "input.gprofiler_type != 'exprs_heatmap'",
                uiOutput("gprofiler_termID")
              ),
              conditionalPanel(
                "input.gprofiler_type=='gostplot' | input.gprofiler_type=='gosttable'",
                numericInput("gprofiler_tbfontsize", "Fontsize:", value = 10,  min = 0, width = "100%"),
                selectInput("gprofiler_showLink", "Show Link in bottom:", choices = c("FALSE", "TRUE"), width = "100%"),
                pickerInput("gprofiler_showColumns", "Columns will be showed:", width = "100%", multiple = T,
                            choices = c("source", "term_name", "term_size", "intersection_size"),
                            selected = c("source", "term_name", "term_size", "intersection_size"))
              ),
              conditionalPanel(
                "input.gprofiler_type == 'exprs_heatmap'",
                uiOutput("gprofiler_termID2"),
                uiOutput("gprofiler_exprs_group"),
                selectInput("gprofiler_data_use", "Values Used To Visualize:", width = "100%",
                            c("rlog or vst transformed value" = "trans_value", "log2(normalized_counts + 1)" = "rel_value",
                              "DESeq2 normalized counts" = "norm_value"))
              ),
              actionButton("gprofiler_plot_modal_but", "Additional Parameters ...", width = "100%",
                           style = "background-color: rgb(255,255,255);text-align:left;margin-bottom:10px", icon = icon("plus-square")),
              disabled(actionButton("Plot_gprofiler", "Plot gProfiler", class = "plot-button", width = "100%"))
            ),
            bsModal(
              "gprofiler_plot_modal",  "Additional Parameters", "gprofiler_plot_modal_but", size = "large",
              fluidPage(
                style = "text-align:justify;color:black;background-color:lavender;border-radius:10px;border:1px solid black;",
                conditionalPanel(
                  "input.gprofiler_type=='dotplot'",
                  h2("Additional Parameters of 'Volcano Plot':"), hr(),
                  textAreaInput("gprofiler_dotplot_ggText", "ggplot2 codes:", value = 'theme(axis.title = element_text(size = 21, face = "bold", color = "black", family = "Times"),
                  axis.text = element_text(size = 18, face = "bold", color = "black", family = "Times"),
                  text = element_text(size = 18, face = "bold", color = "black", family = "Times"))', width = "100%", rows = 12)
                ),
                conditionalPanel(
                  "input.gprofiler_type=='gostplot'",
                  h2("Additional Parameters of 'Volcano Plot':"), hr(),
                  textAreaInput("gprofiler_gostplot_ggText", "ggplot2 codes:", value = 'theme(axis.title = element_text(size = 21, face = "bold", color = "black", family = "Times"),
                  axis.text = element_text(size = 18, face = "bold", color = "black", family = "Times"),
                  text = element_text(size = 18, face = "bold", color = "black", family = "Times"))', width = "100%", rows = 12)
                ),
                conditionalPanel(
                  "input.gprofiler_type=='gosttable'",
                  h2("Additional Parameters of 'Volcano Plot':"), hr(),
                  textAreaInput("gprofiler_gosttable_ggText", "ggplot2 codes:", value = 'theme(axis.title = element_text(size = 21, face = "bold", color = "black", family = "Times"),
                  axis.text = element_text(size = 18, face = "bold", color = "black", family = "Times"),
                  text = element_text(size = 18, face = "bold", color = "black", family = "Times"))', width = "100%", rows = 12)
                ),
                conditionalPanel(
                  "input.gprofiler_type == 'exprs_heatmap'",
                  h2("Additional Parameters of 'DE Heatmap':"), hr(),
                  conditionalPanel(
                    "input.gprofiler_heat_colname",
                    selectInput("gprofiler_heat_angle", "Column names angle (if showed):", choices = c('0', '45', '90', '270', '315'), selected = '315', width = "100%")
                  ),
                  numericRangeInput("gprofiler_cluster_break", "Color bar value:", value = c(-2,2), width = "100%"),
                  numericInput("gprofiler_heatmap_fontsize", "Fontsize:", value = 15, width = "100%")
                )
              )
            ),
            column(
              6,
              wellPanel(
                style = "padding-top:5px",
                fluidRow(
                  column(
                    12, style = "padding-left:0px;margin-left:0px;padding-right:0px;margin-right:0px;border-bottom:solid 1px rgb(224,224,224)",
                    column(
                      6, style = "padding-left:10px;",
                      tags$h4("Enrichment Results Visualization:")
                    ),
                    column(
                      6, align = "right", style = "padding-top:5px;",
                      dropdownButton(
                        numericInput('gprofiler_width', 'Figure Width:', min = 1, max = 20, value = 12, width = "100%"),
                        numericInput('gprofiler_height', 'Figure Height:', min = 1, max = 20, value = 6, width = "100%"),
                        downloadButton('gprofiler_Pdf','Download .pdf', class = "btn btn-warning", width = "100%"),
                        circle = FALSE, status = "danger", size = "sm", icon = icon("save"), width = "200px",
                        right = TRUE, tooltip = tooltipOptions(title = "Click to download figures !")
                      )
                    )
                  )
                ),
                uiOutput("gprofilerPlotUI")
              )
            ),
            column(
              2,
              wellPanel(
                sliderInput("gprofiler_plot_width", "Figure Width (%):", min = 50, max = 100, value = 100, step = 2, width = "100%"),
                sliderInput("gprofiler_plot_height", "Figure Height (px):", min = 200, max = 1000, value = 438, step = 2, width = "100%")
              ),
              conditionalPanel(
                "input.gprofiler_type == 'exprs_heatmap'",
                wellPanel(
                  checkboxInput("gprofiler_heat_rowname", "Showing rownames ?", value = TRUE, width = "100%"),
                  checkboxInput("gprofiler_heat_colname", "Showing colnames ?", value = FALSE, width = "100%")
                )
              )
            )
          )
        ),
        tabPanel(
          "Enrichment Results Table",
          fluidPage(
            style = "padding-top: 5px; padding-left: 0px; padding-right: 0px;margin-left: 0px; margin-right: 0px;",
            uiOutput("sourceID"),
            withSpinner(dataTableOutput("gProfiler_Tab")),
            downloadButton('gprofiler_csv','Download .csv', class = "btn", width = "20%")
          )
        )
      )
    )
  ),
  column(
    12,
    fluidRow(
      style = "background-color: rgb(248,249,250); border: 1px solid rgb(218,219,220); padding: 5px; margin:5px; border-radius: 15px;",
      column(
        4, style = "text-align:center;border-right: 2px solid white; padding-top:15px",
        tags$img(src = "images/demo/gProfiler_Plot.png",
                 width = "100%")
      ),
      column(
        8, style = "text-align:justify;",
        h3("What is g:Profiler ?"),
        p("g:Profiler is a public web server for characterising and manipulating gene lists.
          The R package gprofiler2 provides an R interface to the g:Profiler tools. 
          g:Profiler is developed and maintained in Estonia, at the University of Tartu, 
          Institute of Computer Science, Bioinformatics, Algorithmics and Data Mining Group BIIT. 
          Currently g:Profiler is developed and maintained by a team of professional software developers, statistician and researchers."),
        h3("Why should we use g:Profiler ?"),
        p(
          tags$li("Currently available for 400+ species, including mammals, plants, fungi, insects from Ensembl and Ensembl Genomes."),
          tags$li("g:Profiler is updated approximately in every three months and follows quarterly releases of Ensembl databases."),
          tags$li("g:Profiler supports up to 8 acknowledge database, including Gene Ontology, KEGG, Reactome, WikiPathways, miRTarBase, etc.")
        )
      )
    )
  ),
  column(
    12,
    hr(),
    fluidRow(
      style = "margin-bottom:20px",
      column(3, align = "right", actionLink("pGprofiler", "<< Previous", style = "font-size: 20px")),
      column(6, align = "center"),
      column(3, align = "left", actionLink("nGprofiler", "Next >>", style = "font-size: 20px"))
    )
  )
)