visualize_custom_gene_sets.Rmd

```{r}
library(shiny)
library(visNetwork)
options(shiny.trace = TRUE)
```
# Custom protein sets
##  {.sidebar data-width="200" .opening-page-text}

#### Legend
<p class='options-text'><b>Kinase groups by color</b></p>
```{r}
imageOutput('legend3',height="auto")
output$legend3 <- renderImage({
  list(src='img/kinase_families_legend2.png',width="100%",padding="0px 0px 5px 0px")
},deleteFile=FALSE)
```

#### Include more proteins
```{r,cache=FALSE}
checkboxInput(inputId='toggleOneDegree3', "Proteins adjacent to selected set", value = FALSE)
checkboxInput(inputId='toggleDisconnected3', "Proteins with no interactions", value = FALSE)
```

#### Layout 
```{r,cache=FALSE}
  selectizeInput('layout3',label=NULL,choices=names(layout_choices),selected="Default",multiple=FALSE)
```

#### Export
```{r, cache=FALSE}
  selectizeInput('download_choice3',label=NULL,choices=names(export_choices))
  filename3 <- reactive({export_choices[[input$download_choice3]]})
  (downloadButton('download3',"Download"))
  
  output$download3 <- downloadHandler(
    filename=function() {paste(c('custom',filename3(), collapse='_'))},
    content = function(file) {export_method(filename3(),g3(),file)}
  )
```

## Main Panel {data-width=750}
#### Provide a custom set of proteins {.opening-page-text}
Visualize kinase-substrate interactions within any protein set. Paste a set of gene symbols in the text box below, then click Submit.

<p class='options-text'>
If the selected set does not include any interactions, you may not see any nodes or edges. Use the sidebar options to <b>include more proteins</b>.
</p>

  
```{r,cache=FALSE}


textAreaInput('customGeneList', label=NULL, value = NULL, height="100px",width = "98%")
actionButton('submit', "Submit")
actionButton('example',"Load an example")
actionButton('clear',"Clear")
initialGeneList3 <- reactiveVal('')
notFound <- reactiveVal(c())

textOutput('displayNotFound',inline=TRUE)
output$displayNotFound <- renderText({
  if(length(notFound())==0) {""} else {paste(c("Warning! Genes not found: ",notFound()))}
})

default_gene_set <- "EGFR INSR MAPK1 GAB1 IRS1 PTPN1"

observeEvent(input$example,{updateTextAreaInput(session,'customGeneList', value=paste(default_gene_set))})
observeEvent(input$clear,{updateTextAreaInput(session,'customGeneList', value="")})

observeEvent(input$submit,{
  s <- gsub(",","",toupper(isolate(input$customGeneList)))
  genes <- unique(base::scan(text=s,what=""))
  initialGeneList3(intersect(genes,all_nodes$GeneName))
  notFound(setdiff(genes,all_nodes$GeneName))
  })

```
##### {}
### {}
```{r,cache=FALSE}
g3 <- reactive({get_pathway_graph(initialGeneList3(),input$toggleOneDegree3,input$toggleDisconnected3)})
visNetworkOutput('network3')
output$network3 <- renderVisNetwork({
  vis_default(g3()) %>%
  visEvents(select="function(nodes){Shiny.onInputChange('selectNode3',nodes.nodes);}") %>%
  visEvents(doubleClick="function(nodes){Shiny.onInputChange('nextCenterNode',nodes.nodes)}") %>%
  visEvents(selectEdge = "function(edges) {Shiny.setInputValue('selectedEdges3', edges);}") %>%
  visIgraphLayout(layout=layout_choices[[input$layout3]])
   })

infoGene3 <- reactive({
  if(is.null(input$selectNode3)) {NULL} else {get_gene_name(input$selectNode3)}
  })

infoEdge3 <- reactive({
    req(input$selectedEdges3)
    req(input$selectedEdges3$edges)
    req(g3())
    req(g3()$edges)
    edge_id <- input$selectedEdges3$edges
    e <- g3()$edges %>% filter(id == edge_id)
    req(nrow(e)==1)
    render_edge_info(e)
})

```

##  {data-width="650" .opening-page-text}
### {data-height="500"}
#### Interaction information
<p class='options-text'> <b> Click on an edge</b> </p>

```{r,cache=FALSE}
  renderUI({infoEdge3()})
```
### {data-height="140"}
#### Troubleshooting
<div class="options-text">

<p><b>Not laid out as expected? </b></p>
<p>Try a different layout, or, manually move nodes around.</p>
  
<p><b>Not seeing any interactions?</b></p>
<p>There may be none in the selected set. Use the options provided to <b>include more proteins</b>. </p>
</div>