sqtlviztools: Visualise splicing QTLs

library(shiny)
library(DT)
library(shinycssloaders)
library(shinyjs)

ui <- tagList(
  useShinyjs(),
  navbarPage(
    #title  = actionLink("aboutLink", "LeafViz"),
    title = "sQTLviz",
    #title = a(id = "gitLink", href="https://github.com/davidaknowles/leafcutter/tree/master/leafviz","LeafViz", target = "_blank"),
    id = "navBarPage",
    windowTitle = "sQTLviz",
    tabPanel("example sQTLs",
             value = "resultsToPlot",
             # padding-top: 70px
             tags$style(type="text/css", "
#UCSC_button {
  margin-top: 10px;
  margin-bottom: 10px;
  display: block;
  text-align: center;
}
#UCSC {
  border-color: #ccc;
  color: #333;
}

#UCSC:hover {
  background-color: #E6E6E6;
}

#titlePanel {
  text-align: center;
}

#logo {
    margin: 0 auto;
    width: 4%;
    position: fixed;
    z-index: -1;
}

#title {
    size:huge;
}

")),
    tabPanel("About", value = "NA",

             fluidRow(id = "tabDiv",
                      column(
                        6,
                        offset=3,
                        div(
                          h2("What is this?"),
                          p( "This R", tags$a(href="https://shiny.rstudio.com","Shiny", target = "_blank"),
                             "app presents and visualises splicing quantitative trait loci (sQTLs) discovered in 450 human frontal cortex samples.",
                             "Samples were provided by the ROS/MAP Consortium.",
                             "Data is available through the RUSH Alzheimer’s Disease Research Center Research Resource Sharing Hub",
                             a(href="https://www.radc.rush.edu", "here.", target = "_blank")
                            ),
                          h2( "Differential splicing events"),
                          p( "A cluster is defined as set of overlapping spliced junctions or introns.",
                             "Clusters are initially ranked in the cluster results table by adjusted P value."
                          ),
                          tags$ul(
                            tags$li( strong("SNP -") , "the rs ID of the single nucleotide polymorphism (SNP)." ),
                            tags$li( strong("Position -") , "the genomic coordinates (hg19) of the single nucleotide polymorphism (SNP)." ),
                            tags$li( strong("Gene -"), "the HUGO gene sympbol for that gene."),
                            tags$li( strong("Cluster coordinates - "), "the coordinate span of the the cluster."  ),
                            tags$li( strong("q -"), "the Benjamini-Hochberg adjusted P value of the multinomial test of intron counts between conditions.")
                          ),
                          h2("Splicing event visualization"),
                          p("To view a cluster, click on a row in the cluster results table. This will start the plotting function.",
                            "A cluster plot and table are generated each time a row in the cluster results is clicked."
                          ),
                          p("For a chosen cluster, the mean number of splice junctions supporting each intron is calculated for each genotype and then normalised as a fraction of the total counts.",
                            "Therefore for each condition the normalised counts will add up to 1.",
                            "Each intron is plotted as a line connecting its start and end coordinates with a thickness proportional to the displayed normalised count value.",
                            "The colour of the intron line indicates whether it is present in the annotation (red) or not (pink).",
                            "Any exons that are annotated as flanking or being contained within the cluster are added as rectangles to the plot.",
                            "If exons from multiple genes are connected by introns then their exons will be coloured according to their gene of origin."
                          ),
                          p("Each intron is presented as a row in the cluster view table."
                          ),
                          tags$ul(
                            tags$li( strong("chr, start, end"), "the genomic coordinates of the intron." ),
                            tags$li( strong("verdict") , "the support given to two splice sites of the intron (start and end) by annotation." ),
                            tags$ul(
                              tags$li( em("annotated -"), "both splice sites are present in an annotated junction"),
                              tags$li( em("novel annotated pair -"), "both splice sites are annotated but are not annotated as being paired in a junction"),
                              tags$li( em("cryptic_fiveprime -"), "the 3\' splice site is annotated but the 5\' is not."),
                              tags$li( em("cryptic_threeprime -"), "the 5\' splice site is annotated but the 3\' is not ")
                            )
                          ),

                          h2("Gene-level visualization"),
                          p("This visualises all clusters discovered by Leafcutter that can be assigned to a particular gene.",
                            "Exons are taken from the provided annotation and plotted as black rectangles.",
                            "Each junction in each cluster is plotted as curved line with uniform thickness.",
                            "Note that the genomic coordinates are deliberately warped to give more space to the clusters."
                          ),

                          h2("Junction-level visualization"),
                          p("The junction with the most significant association to the SNP is bolded in the cluster-level plot.",
                            "As well, the contribution of that junction to the cluster is calculated for each sample and split by genotype.",
                            "The Beta and q values come from the logistic regression."
                          ),

                          h2("Acknowledgments"),
                          p("We thank the participants of ROS and MAP for their essential contributions and gift to these projects.")
                        )
                      )
             )

             ),



  # Application title
  div(id = "titlePanel",
    #HTML("<img id=logo src=squirtle.png>"),
    h1("sQTLviz: explore splicing QTLs", id = "titlePanel")
    ),


    fluidRow(
      column(8,offset=2,
        div(
          DT::dataTableOutput("all_clusters")
        )
      )
    ),
    withSpinner(div(
      column(7, offset = 1,
        h3(id = "title", "Whole gene visualization")
      ),
      column(12, offset = 0,
        plotOutput("select_gene_plot",width="100%", height = "350px")
      ),
      fluidRow(
        column(7, offset = 1,
          div(
            h3(id = "title", "Cluster visualization"),
            h5(id = "subtitle", "Most significant junction is bolded")
          ),
          div(
           plotOutput("select_cluster_plot", width = "100%", height = "500px")
          )
        ),
        column(3,
          h3(id = "title", "Most significant junction"),
          div(
            plotOutput("select_box_plot", width = "100%", height = "500px")
          )
        )
      ),
      fluidRow(
        column(8,offset=2,
          div(
        DT::dataTableOutput("junctionTable")
          )
        )
      ),
      div( id = "UCSC_button",
           htmlOutput("view_cluster_UCSC", inline = TRUE)
           )
    ), type = 8
    )
  )
)