inst/shiny_app/ui/tabPlots/tabSetVolcano.R

In svalvaro/MQanalyser: Analyse the proteomics LC-MS/MS data from MaxQuant.

tabSetVolcano <-  tabPanel(h4('Volcano Plot'),
                           value = 'volcano-tab',
                           sidebarLayout(
                               sidebarPanel(
                                   id = 'sidebar',
                                   width = 2,
                                   h3("Select the adjustments"),

                                   uiOutput("comparisons_out"),

                                   dropdown(
                                       tags$h3("Advanced Parameters"),


                                       #check box for protein IDs
                                       checkboxInput(
                                           inputId = 'modify_axis',
                                           label = h4(
                                               'Would you prefer to modify the
                          axis values: \n(Uncheck to restore values)'
                                           ),
                                           value = FALSE
                                       ),

                                       conditionalPanel(
                                           "input.modify_axis == 1",

                                           sliderInput(
                                               inputId = 'range_fc',
                                               label = h4('Log2(Fold-Change) Range'),
                                               min = -10,
                                               max = 10,
                                               step = 0.1,
                                               value = c(-6, 6)
                                           ),

                                           sliderInput(
                                               inputId = 'range_pvalue',
                                               label = h4('-Log10(P-Value): Range'),
                                               min = 0,
                                               max = 50,
                                               step = 0.5,
                                               value = c(0, 5)
                                           )
                                       ),
                                       br(),
                                       hr(),
                                       sliderInput(
                                           inputId = 'volc_alpha',
                                           label = 'Adjust the transparency of
                                    the points:',
                                           value = 0.8,
                                           min = 0,
                                           max = 1
                                       ),

                                       #check box for protein IDs
                                       checkboxInput(
                                           inputId = 'p_adj_input',
                                           label = h4('Use adjusted P values'),
                                           value = TRUE
                                       ),

                                       #Select the Colour for UPregulated
                                       colourpicker::colourInput(
                                           "col_upregulated",
                                           h4("Colour upregulated:"),
                                           'brown2',
                                           palette = "square",
                                           returnName = TRUE,
                                           showColour = c("background")
                                       ),

                                       #Select the color for Down regulated
                                       colourpicker::colourInput(
                                           "col_downregulated",
                                           h4("Colour downregulated:"),
                                           'cyan3',
                                           palette = "square",
                                           returnName = TRUE,
                                           showColour = c("background")
                                       ),

                                       #Select the color for selected genes
                                       colourpicker::colourInput(
                                           "col_selected",
                                           h4("Colour your proteins of interest:"),
                                           '#800080',
                                           palette = "square",
                                           returnName = TRUE,
                                           showColour = c("background")
                                       ),

                                       options = list(`style` = "btn-info"),
                                       style = "unite",
                                       icon = icon("paint-brush"),
                                       status = "success",
                                       width = "300px",
                                       animate = animateOptions(
                                           enter = animations$fading_entrances$fadeInLeftBig,
                                           exit = animations$fading_exits$fadeOutRightBig
                                       )
                                   ),
                                   hr(),

                                   tags$div(
                                       title = "Press ON if you would like to see the gene names. Draw a box around the genes that you are interested in",

                                       shinyWidgets::switchInput(
                                           inputId = "showGeneNames",
                                           label = "Gene Names",
                                           labelWidth = "80px",
                                           onStatus = 'success',
                                           value = TRUE,
                                           offStatus = 'danger'
                                       )
                                   ),

                                   # Font size depending on the showGeneNames:

                                   uiOutput('font_gene_labels'),

                                   hr(),
                                   #Check box for fav genes
                                   checkboxInput(
                                       inputId = 'showgenes_volcano',
                                       label = h4('Show your selected genes'),
                                       value = FALSE
                                   ),

                                   #Download button for the volcano plot
                                   #downloadButton('downloadvolcano','Download the Volcano Plot')
                                   uiOutput('downloaderVolcano')
                               ),

                               mainPanel(box(
                                   shinycssloaders::withSpinner(
                                       uiOutput('volcano_final'),
                                       #plotlyOutput('volcano_plot'),
                                       image = 'images/logoTransparentSmall.gif',
                                       image.width = '200px'
                                   )
                               ))
                           )
                           )