R/modules/visualization/visualization.R

In benhid/Rpath: A Web-App for Biologic Pathway Exploration

source('modules/visualization/parseSifInteractionsView.R', local = TRUE)

output$binaryGraph <- renderVisNetwork({
  nodes <- data.frame(label="", group="", id="", stringsAsFactors=FALSE)
  edges <- data.frame(from="", title="", to="", stringsAsFactors=FALSE)

  tryCatch({
    withProgress(message = 'Loading', value = 0, {
      incProgress(0.1, detail = paste("Getting binary SIF"))

      URL <- getRowFromDf()
      owl <- getPc(URL)

      incProgress(0.5, detail = paste("Parsing..."))

      edges <- toSif(owl)
      colnames(edges) <- c("from", "title", "to")

      incProgress(0.8, detail = paste("Parsing..."))

      sifnx <- toSifnx(owl)
      nodes <- sifnx$nodes[, 1:2]
      nodes$id <- nodes$PARTICIPANT
      colnames(nodes) <- c("label", "group", "id")
    })
  }, error = function(e){
    showNotification("Sorry, your graph couldn't be displayed propertly.", type = "error")
  })

  title <- as.character(finalSearchResultsDf$name[input$searchResults_rows_selected])

  visNetwork(nodes, edges, width = "100%", directed = TRUE, main = title) %>%
    visEdges(arrows="to", smooth="false") %>%
    visGroups(groupname = "SmallMoleculeReference", shape = "square") %>%
    visGroups(groupname = "ProteinReference", shape = "dot") %>%
    visLayout(randomSeed = 12) %>%
    visPhysics(enabled=FALSE) %>%
    visOptions(nodesIdSelection = TRUE, highlightNearest = list(enabled = T, degree = 1, hover = T))
})

output$extendedGraph <- renderVisNetwork({
  nodes <- data.frame(label="", group="", id="", stringsAsFactors=FALSE)
  edges <- data.frame(from="", title="", to="", stringsAsFactors=FALSE)

  tryCatch({
    withProgress(message = 'Loading', value = 0, {
      incProgress(0.1, detail = paste("Getting extended SIF"))

      URL <- getRowFromDf()
      owl <- getPc(URL)
      sifnx <- toSifnx(owl)

      incProgress(0.5, detail = paste("Parsing..."))

      links <- parseSifInteractionsVisNetwork(sifnx)

      edges <- data.frame(links$source, links$tipoLink, links$target)
      colnames(edges) <- c("from", "title", "to")

      incProgress(0.8, detail = paste("Parsing..."))

      nodes <- data.frame(links$nodos,links$tipoNodo)
      nodes <- nodes[!duplicated(nodes),]
      nodes$id <- nodes$links.nodos
      colnames(nodes) <- c("label", "group", "id")
    })
  }, error = function(e){
    showNotification("Sorry, your graph couldn't be displayed propertly.", type = "error")
  })

  title <- as.character(finalSearchResultsDf$name[input$searchResults_rows_selected])

  visNetwork(nodes, edges, width = "100%", directed = TRUE) %>%
    visEdges(arrows="to", smooth="false") %>%
    visGroups(groupname = "NProt", shape = "dot", color = "darkblue") %>%
    visGroups(groupname = "control", shape = "square", color = "purple") %>%
    visGroups(groupname = "chemical", shape = "dot", color = "grey") %>%
    visGroups(groupname = "state", shape = "dot", color = "darkred") %>%
    visGroups(groupname = "phospho", shape = "dot", color = "orange") %>%
    visGroups(groupname = "Common", shape = "dot", color = "green") %>%
    visGroups(groupname = "NSM", shape = "dot") %>%
    visLayout(randomSeed = 12) %>%
    visPhysics(enabled=FALSE) %>%
    visOptions(nodesIdSelection = TRUE, highlightNearest = list(enabled = T, degree = 1, hover = T))
})

source('modules/visualization/parseSifInteractionsD3.R', local = TRUE)

observeEvent(input$buttonGraph, {
  withProgress(message = 'Loading', value = 0, {
    incProgress(0.1, detail = paste("Getting extended SIF"))

    URL <- getRowFromDf()
    owl <- getPc(URL)

    sifnx <- toSifnx(owl)

    insertUI(
      selector = "#graph",
      where = "afterEnd",
      ui = tags$div(id="graph", class="paintGraph")
    )

    incProgress(0.5, detail = paste("Parsing..."))
    links <- parseSifInteractionsD3(sifnx)

    incProgress(0.8, detail = paste("Parsing..."))
    js$paintGraph(links)
  })
})

observeEvent(input$deleteGraph, {
  removeUI(
    selector = "div#graph"
  )
})