inst/shiny/modules/12.2-ui-wgcna-expression.R

In goushixue/QRseq: Quickly RNA-seq Analysis Platform

fluidRow(
  style = "margin-left: 10px; margin-right:10px;",
  box(
    title = "Plotting Parameters:", width = 4, collapsible = TRUE, solidHeader = TRUE,
    prettyRadioButtons(inputId = "wgcna_exp_ptype", label = "Visualization method:", animation = "jelly", inline = TRUE,
                       choices = c("Pheatmap", "BarPlot"), icon = icon("check"), status = "info"),
    uiOutput("wgcna_exp_trait"),
    uiOutput("wgcna_exp_module"),
    conditionalPanel(
      "input.wgcna_exp_ptype == 'Pheatmap'",
      uiOutput("wgcna_exp_anno"),
      numericInput("wgcna_hiera_fontsize", "Fontsize:", value = 15, width = "100%"),
      textInput("wgcna_hiera_color", "color:", value = "navy,white,red", placeholder = "eg. navy,white,red or #000080,#FFFFFF,#FF0000", width = "100%")
    ),
    conditionalPanel(
      "input.wgcna_exp_ptype == 'BarPlot'",
      numericInput("wgcna_bar_cex", "Fontsize of base:", value = 18, width = "100%"),
      numericInput("wgcna_bar_lab", "Fontsize of label text:", value = 18, width = "100%"),
      numericInput("wgcna_bar_axis", "Fontsize of axis text:", value = 12, width = "100%"),
    ),
    actionButton("wgcna_expr_modal_but", "Additional Parameters ...", width = "100%",
                 style = "background-color: rgb(255,255,255);text-align:left; margin-bottom:10px", icon = icon("plus-square")),
    br(),
    actionButton("wgcna_plot_exp", "Plot Module-Traits Relationship Heatmap", width = "100%", class = "plot-button")
  ),
  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("Visualization of genes expression in Module:")
          ),
          column(
            6, align = "right", style = "padding-top:5px;",
            dropdownButton(
              numericInput('wgcna_exp_width', 'Figure Width:', value = 7, width = "100%"),
              numericInput('wgcna_exp_height', 'Figure Height:', value = 7, width = "100%"),
              downloadButton('wgcna_exp_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("wgcna_expressionUI")
    )
  ),
  column(
    2,
    wellPanel(
      sliderInput("wgcna_expression_width", "Figure Width (%):", min = 50, max = 100, value = 100, step = 2, width = "100%"),
      sliderInput("wgcna_expression_height", "Figure Height (px):", min = 200, max = 1000, value = 511, step = 2, width = "100%")
    )
  ),
  bsModal(
    "wgcna_expr_modal", "Additional Parameters", "wgcna_expr_modal_but", size = "large",
    fluidPage(
      style = "text-align:justify;color:black;background-color:lavender;border-radius:10px;",
      h3("Additional Parameters:"), hr(),
      conditionalPanel(
        "input.wgcna_exp_ptype == 'Pheatmap'",
        checkboxInput("wgcna_hiera_colname", "show column names ?", value = FALSE, width = "100%"),
        conditionalPanel(
          "input.wgcna_hiera_colname",
          selectInput("wgcna_hiera_angle", "Column names angle (if showed):", choices = c('0', '45', '90', '270', '315'), selected = '315', width = "100%")
        )
      ),
      conditionalPanel(
        "input.wgcna_exp_ptype == 'BarPlot'",
        textAreaInput("wgcna_expr_ggText", "ggplot2 codes:", value = 'theme(axis.title = element_text(face = "bold", color = "black", family = "Times"),
        axis.text = element_text(face = "bold", color = "black", family = "Times"),
        text = element_text(face = "bold", color = "black", family = "Times"))', width = "100%", rows = 12)
      )
    )
  ),
  column(
    12, style = "padding:0px;",
    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/wgcna_heatmap.png",
                 width = "100%")
      ),
      column(
        8, style = "text-align:justify;",
        h3("What is Module eigengenes (ME) ?"),
        p("ME can be considered the most representative gene expression profile of the module.
          We can create a plot that explains the relationships between modules (heatmap) and the corresponding module eigengene (barplot).
          Note that the module eigengene takes on low values in arrays where a lot of module genes are under-expressed (blue color in the heatmap). 
          The ME takes on high values for arrays where a lot of module genes are over-expressed (red in the heatmap).
          In the Module heatmap, the rows correspond to genes and the columns to samples; blue denotes under-expression and red over-expression.
          the Module barplot shows the corresponding module eigengene expression values (y-axis) versus the same samples (x-axis)."),
        p("For example, the heatmap on the left shows the eigengenes expression of module turquoise versus the samples that ordered by
          HFD45 (hospital-free days at day 45) score of COVID-19 patients. Obviously, the expression of genes in this module 
          are higly positively correlated with HFD45 score, and the expression of these genes increased with the increase of HFD45 score.
          The expression of these genes is significantly related to the reduction of hospitalization days of patients. 
          Indeed, functional enrichment analysis can find that these genes are mainly related to the immune system, 
          so enhancing immunity can reduce the hospitalization days of patients.")
      )
    )
  ),
  column(
    12,
    hr(),
    fluidRow(
      style = "margin-bottom:20px",
      column(3, align = "right", actionLink("pWGCNA_expression", "<< Previous", style = "font-size: 20px")),
      column(6, align = "center"),
      column(3, align = "left", actionLink("nWGCNA_expression", "Next >>", style = "font-size: 20px"))
    )
  )
)