Create a NGLVieweR

NGLVieweR can be used to visualize and interact with Protein Data Bank (PDB) and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation in Shiny.

NGLVieweR(data, format = NULL, width = NULL, height = NULL, elementId = NULL)

Arguments

data

PDB file or PDB entry code

format

Input format (.mmcif, .cif, .mcif, .pdb, .ent, .pqr, .gro, .sdf, .sd, .mol2, .mmtf). Needed when no file extension is provided.

width, height

Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.

elementId

optional element Id

Value

A NGLVieweR htmlwidgets object.

Details

The package is based on the NGL.js JavaScript library. To see the full set of features please read the official manual of NGL.js.

See also

• NGLVieweR_proxy() for handling of API calls after rendering.

• NGLVieweR_example() See example "API" and "basic".

Examples

# Example 1: Most Basic
NGLVieweR("7CID") %>%
 addRepresentation("cartoon", 
 param = list(name = "cartoon", colorScheme="residueindex"))


# Example 2: Advanced
NGLVieweR("7CID") %>%
  stageParameters(backgroundColor = "white") %>%
  setQuality("high") %>%
  setSpin(FALSE) %>%
  addRepresentation("cartoon",
    param = list(
      name = "cartoon",
      colorScheme = "residueindex"
    )
  ) %>%
  addRepresentation("ball+stick",
    param = list(
      name = "ball+stick",
      colorValue = "red",
      colorScheme = "element",
      sele = "200"
    )
  ) %>%
  addRepresentation("label",
    param = list(
      name = "label", sele = "200:A.O",
      showBackground = TRUE,
      backgroundColor = "black",
      backgroundMargin = 2,
      backgroundOpacity = 0.5,
      showBorder = TRUE,
      colorValue = "white"
    )
  ) %>%
  addRepresentation("surface",
    param = list(
      name = "surface",
      colorValue = "white",
      opacity = 0.1
    )
  ) %>%
  zoomMove("200", "200", 2000, -20)


#---------------------Using Shiny-------------------------

# App 1: Basic Example
if (interactive()) {
  library(shiny)
  ui <- fluidPage(NGLVieweROutput("structure"))
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(
            name = "cartoon",
            colorScheme = "residueindex"
          )
        ) %>%
        addRepresentation("ball+stick",
          param = list(
            name = "cartoon",
            sele = "1-20",
            colorScheme = "element"
          )
        ) %>%
        stageParameters(backgroundColor = "black") %>%
        setQuality("high") %>%
        setFocus(0) %>%
        setSpin(TRUE)
    })
  }
  shinyApp(ui, server)
}

# App 2: Example with API calls
if (interactive()) {
library(shiny)

ui <- fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      textInput("selection", "Selection", "1-20"),
      selectInput("type", "Type", c("ball+stick", "cartoon", "backbone")),
      selectInput("color", "Color", c("orange", "grey", "white")),
      actionButton("add", "Add"),
      actionButton("remove", "Remove")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server <- function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", colorScheme = "residueindex")
      ) %>%
      stageParameters(backgroundColor = input$backgroundColor) %>%
      setQuality("high") %>%
      setFocus(0) %>%
      setSpin(TRUE)
  })
  observeEvent(input$add, {
    NGLVieweR_proxy("structure") %>%
      addSelection(isolate(input$type),
        param =
          list(
            name = "sel1",
            sele = isolate(input$selection),
            colorValue = isolate(input$color)
          )
      )
  })

  observeEvent(input$remove, {
    NGLVieweR_proxy("structure") %>%
      removeSelection("sel1")
  })
}
shinyApp(ui, server)
}