examine_proteins.Rmd

```{r}
library(shiny)
library(visNetwork)
```
# Proteins
##  {.sidebar data-width="200" .opening-page-text}
#### Legend
<p class='options-text'><b>Kinase groups by color</b></p>
```{r}
imageOutput('legend',height="auto")
output$legend <- renderImage({
  list(src='img/kinase_families_legend2.png',width="100%")
},deleteFile=FALSE)
```
#### Layout 
```{r,cache=FALSE}
  selectizeInput('layout1',label=NULL,choices=names(layout_choices),selected="Default",multiple=FALSE)
```
#### Export
```{r, cache=FALSE}
  selectizeInput('download_choice1',label=NULL,choices=names(export_choices))
  filename1 <- reactive({export_choices[[input$download_choice1]]})
  (downloadButton('download1',"Download"))
  
   output$download1 <- downloadHandler(
    filename=function() {filename1()},
    content = function(file) {export_method(filename1(),g1(),file)}
  )
```
#### Data Overview {.disclaimer-text}
Last update: </br> <b>`r dataset_last_update`</b>

Proteins available: </br> <b> `r nproteins` </b>

Proteins data source: </br> [UniProt](https://www.uniprot.org/uniprotkb?query=Human&facets=reviewed%3Atrue%2Cmodel_organism%3A9606){target="_blank"} <i>`r uniprot_release`</i>.

## Main Panel {data-width=750}


#### Choose a protein {.opening-page-text}
Visualize kinase-substrate interactions of **individual proteins**. Choose a protein from the dropdown menu, or, double-click on a visible protein node.

```{r, cache = FALSE}
selectizeInput(inputId='centerGene',choices=all_nodes$GeneName,label=NULL,selected = "STK11", multiple = F,options=list(maxOptions=4000))
``` 
### {}
```{r, cache=FALSE}
g1 <- reactive(get_one_degree(input$centerGene,TRUE))
visNetworkOutput('network1')
output$network1 <- renderVisNetwork({
  vis_default(g1()) %>%
  visNodes(scaling=list(label=list(min=60,max=80))) %>%
  visEvents(selectEdge = "function(edges) {Shiny.setInputValue('selectedEdges1', edges.edges);}") %>%
  visEvents(selectNode ="function(nodes){Shiny.onInputChange('selectNode1', nodes.nodes);}") %>%
  visEvents(doubleClick="function(nodes){Shiny.onInputChange('nextCenterNode',nodes.nodes)}") %>%
  visIgraphLayout(layout=layout_choices[[input$layout1]],smooth=T,physics=(nrow(g1()$edges)<10))
   })

observeEvent(input$nextCenterNode,{updateSelectInput(inputId='centerGene',selected=get_gene_name(input$nextCenterNode))})

infoGene1 <- reactive({
  req(input$selectNode1)
  get_gene_name(input$selectNode1)
  # if(is.null(input$selectNode1)) {NULL} else {get_gene_name(input$selectNode1)}

})

infoEdge1 <- reactive({
# infoEdge1 <- renderUI({
    # 
    # req(input$selectedEdges1)
    # input[['button-view-toggle-p1']] <- FALSE
    
    req(input$selectedEdges1)
    print(input$selectedEdges1)
    req(g1())
    req(g1()$edges)
    edge_id <- input$selectedEdges1
    e <- g1()$edges %>% filter(id == edge_id)
    req(nrow(e)==1)
    # render_edge_info(e, 'button-view-toggle-p1', 'seq-table-p1')
    render_edge_info(e)
})

# observeEvent()
```

##  {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({infoEdge1()})
```

<!-- #### test2  -->
<!-- test123 -->

### {data-height="110"}
#### 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>
  
</div>