visualize_domain_enrichments.Rmd

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

#### Legend
<p class='options-text'><b>Kinase groups by color</b></p>
```{r}
imageOutput('legend4',height="auto")
output$legend4 <- 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='toggleOneDegree4', "Proteins adjacent to selected set", value = FALSE)
checkboxInput(inputId='toggleDisconnected4', "Proteins with no interactions", value = FALSE)
```

#### Layout 
```{r,cache=FALSE}
  selectizeInput('layout4',label=NULL,choices=names(layout_choices),selected="Default",multiple=FALSE)
```

#### Export
```{r, cache=FALSE}
  selectizeInput('download_choice4',label=NULL,choices=names(export_choices))
  filename4 <- reactive({export_choices[[input$download_choice4]]})
  (downloadButton('download4',"Download"))
  
  output$download4 <- downloadHandler(
    filename=function() {paste(c(input$domain,filename4()), collapse='_')},
    content = function(file) {export_method(filename4(),g4(),file)}
  )
```

#### Data Overview {.disclaimer-text}
Last update: </br> <b>`r dataset_last_update`</b>

Domains available: </br> <b> `r npathways`</b>

Domains data source: </br> `r interpro_name` gene set library provided by [Enrichr](https://maayanlab.cloud/Enrichr/).

Enrichment analysis software: </br> [GSEApy](https://github.com/zqfang/GSEApy/){target="_blank"} <i>`r gseapy_release`</i>.

For more details,see our [paper](https://doi.org/10.1101/2023.12.08.570875){target="_blank"}.


## Main Panel {data-width=750}
#### Choose a domain {.opening-page-text }

Visualize kinase-substrate interactions among proteins with select [InterPro](https://www.ebi.ac.uk/interpro/){target="_blank"} **domains**.  Choose a domain from the dropdown menu.

<p class='options-text'>
Domains were selected by enriching their protein sets against substrates in the KiNet interaction dataset. If a domain is only present in kinase substrates, you may not see any nodes or edges. Use the sidebar options to <b>include more proteins</b>.
</p>


```{r, cache = FALSE}
selectizeInput(inputId='domain',label=NULL,choices=all_domains,selected="SH3 domain",options=list(maxOptions=200))
initialGeneList4 <- reactive({get_domain_genes(input$domain)})
```

### {}
```{r,cache=FALSE}
g4 <- reactive({get_pathway_graph(initialGeneList4(),input$toggleOneDegree4,input$toggleDisconnected4)})
visNetworkOutput('network4')
output$network4 <- renderVisNetwork({
  vis_default(g4()) %>%
  visEvents(select="function(nodes){Shiny.onInputChange('selectNode4',nodes.nodes);}") %>%
  visEvents(doubleClick="function(nodes){Shiny.onInputChange('nextCenterNode',nodes.nodes)}") %>%
  visEvents(selectEdge = "function(edges) {Shiny.setInputValue('selectedEdges4', edges);}") %>%
  visIgraphLayout(layout=layout_choices[[input$layout4]])
   })

infoGene4 <- reactive({
  if(is.null(input$selectNode4)) {NULL} else {get_gene_name(input$selectNode4)}
  })

infoEdge4 <- reactive({
    req(input$selectedEdges4)
    req(input$selectedEdges4$edges)
    req(g4())
    req(g4()$edges)
    edge_id <- input$selectedEdges4$edges
    e <- g4()$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({infoEdge4()})
```
### {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>