Package {NGLVieweR}

Create a NGLVieweR

Description

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.

Usage

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

Arguments

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.

Value

A NGLVieweR htmlwidgets object.

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 = "ball+stick",
            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$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", colorScheme = "residueindex")
      ) %>%
      stageParameters(backgroundColor = "black") %>%
      setQuality("high") %>%
      setFocus(0) %>%
      setSpin(TRUE)
  })
  observeEvent(input$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)
}

Shiny bindings for NGLVieweR

Description

Output and render functions for using NGLVieweR within Shiny applications and interactive Rmd documents.

Usage

NGLVieweROutput(outputId, width = "100%", height = "400px")

renderNGLVieweR(expr, env = parent.frame(), quoted = FALSE)

NGLVieweR_proxy(id, session = shiny::getDefaultReactiveDomain())

Arguments

Value

NGLVieweR object that can be placed in the UI.

See Also

NGLVieweR_example()

Examples

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$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", color = "residueindex")
      ) %>%
      stageParameters(backgroundColor = "black") %>%
      setQuality("high") %>%
      setFocus(0) %>%
      setSpin(TRUE)
  })
  observeEvent(input$add, {
    NGLVieweR_proxy("structure") %>%
      addSelection(isolate(input$type),
        param =
          list(
            name = "sel1",
            sele = isolate(input$selection),
            color = isolate(input$color)
          )
      )
  })

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

Run NGLVieweR example Shiny app

Description

Launch an example to demonstrate how to use NGLVieweR in Shiny.

Usage

NGLVieweR_example(example = "basic")

Arguments

Value

Call to load Shiny example.

Examples

if (interactive()) {

# Basic example
NGLVieweR_example("basic")

# Example with API calls
NGLVieweR_example("API")

# Function specific example
NGLVieweR_example("addSelection")
}

Add representation

Description

Add a representation and its parameters.

Usage

addRepresentation(NGLVieweR, type, param = list())

Arguments

Details

type and param are passed to NGL.js as they are, so every NGL.js representation and parameter works, including ones not listed above. Some useful ones:

• Other styles: "spacefill", "licorice", "hyperball", "backbone", "trace", "tube", "rope", "rocket", "point", "axes", "helixorient", "unitcell" and "contact".

• Measurements: "distance" (atomPair), "angle" (atomTriple) and "dihedral" (atomQuad). Give each as a list of selections, e.g. atomPair = list(list("1.CA", "20.CA")). These are only drawn; the measured values are not returned to R or Shiny.

• Biological assemblies and crystal packing: the assembly parameter shows a biological unit such as "BU1", the unit cell ("UNITCELL") or a 3x3x3 block of unit cells ("SUPERCELL"). The default is the asymmetric unit ("AU"). Only assemblies defined in the file can be shown.

Value

List of representation parameters to NGLVieweR htmlwidgets object.

See Also

• addSelection()

• NGLVieweR_example() See example "basic".

Examples

NGLVieweR("7CID") %>%
  stageParameters(backgroundColor = "black") %>%
  addRepresentation("cartoon", 
  param = list(name = "cartoon", colorValue = "blue")) %>%
  addRepresentation("ball+stick",
    param = list(
      name = "ball+stick", sele = "241",
      colorScheme = "element", colorValue = "yellow"
    ) 
  ) %>%
  addRepresentation("label",
    param = list(
      name = "label",
      showBackground = TRUE,
      labelType = "res",
      color = "black",
      backgroundColor = "white",
      backgroundOpacity = 0.8,
      sele = ":A and 241 and .CG"
    )
  )

# Biological assembly
NGLVieweR("1RUZ") %>%
  addRepresentation("cartoon", param = list(assembly = "BU1"))

# Distance measurement
NGLVieweR("1CRN") %>%
  addRepresentation("cartoon") %>%
  addRepresentation("distance",
    param = list(atomPair = list(list("1.CA", "20.CA")))
  )

# Shiny context
if (interactive()) {
  library(shiny)
  ui <- fluidPage(NGLVieweROutput("structure"))
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        stageParameters(backgroundColor = "black") %>%
        addRepresentation("cartoon",
          param = list(name = "cartoon", colorValue = "blue")
        ) %>%
        addRepresentation("ball+stick",
          param = list(
            name = "ball+stick", sele = "241",
            colorScheme = "element"
          )
        ) %>%
        addRepresentation("label",
          param = list(
            name = "label",
            showBackground = TRUE,
            labelType = "res",
            colorValue = "black",
            backgroundColor = "white",
            backgroundOpacity = 0.8,
            sele = ":A and 241 and .CG"
          )
        )
    })
  }
  shinyApp(ui, server)
}

Add a selection

Description

Add a new selection to a NGLVieweR object in Shinymode.

Usage

addSelection(
  NGLVieweR_proxy,
  type,
  param = list(),
  structureIndex = NULL,
  structure = NULL
)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• updateRepresentation() Update an existing NGLVieweR representation.

• NGLVieweR_example() See example "addSelection".

Other selections: removeSelection(), updateSelection()

Examples

## Not run: 
NGLVieweR_proxy("7CID") %>%
 addSelection("ball+stick", param = list(name="sel1",
                                         sele="1-20",
                                         colorValue="yellow",
                                         colorScheme="element"
                                         ))

## End(Not run)

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$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", colorScheme = "residueindex")
      )
  })
  observeEvent(input$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)
}

Add structure

Description

Add a structure to the NGLVieweR object, either from a PDB entry code, a file, or directly from the R environment.

Usage

addStructure(NGLVieweR, data, format = NULL)

Arguments

Details

This function allows you to add a structure to the NGLVieweR widget. You can add the structure using a PDB entry code, by specifying a local file, or by providing the structure data directly. If the format is not clear from the input, you may need to specify it using the format parameter.

Value

An updated NGLVieweR object with the added structure.

Examples

NGLVieweR("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "blue")) %>%
  addStructure("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "orange")) %>%
  setPosition(x = 20, y = 0, z = 0) %>%
  setRotation(x = 2, y = 0, z = 0, degrees = FALSE) %>% 
  setScale(0.5)

# Note: The first "1CRN" structure is represented in blue, while the second 
# "1CRN" structure is represented in orange. Transformations such as 
# setPosition, setRotation, and setScale apply to the second 
# (most recently added) structure.

Color residues by value

Description

Color residues by a numeric value computed in R, such as a conservation score, a mutation effect or a p-value. The values are mapped onto a color gradient, and the result can be used as color wherever a representation takes one: addRepresentation, addSelection, updateColor and updateRepresentation.

Usage

colorByValue(
  values,
  palette = c("blue", "white", "red"),
  domain = NULL,
  na_color = "grey"
)

Arguments

Details

The colors are computed in R, so the viewer shows exactly the colors that grDevices::colorRamp(palette) gives. A row for a specific chain or structure takes precedence over a row for any chain or structure. NGL.js cannot show a color legend; the returned object contains palette and domain (as HEX colors and numbers) so a legend can be drawn next to the viewer, e.g. with a plot.

Value

A NGLVieweR_colorByValue object to use as color.

See Also

addRepresentation(), updateColor(), NGLVieweR-shiny

Examples

scores <- data.frame(chain = "A", resno = 1:46, value = sin(1:46 / 5))
NGLVieweR("1CRN") %>%
  addRepresentation("cartoon",
    param = list(color = colorByValue(scores,
                                      palette = c("blue", "white", "red"),
                                      domain = c(-1, 1))))

# A named vector, for a few residues; all others are grey
NGLVieweR("1CRN") %>%
  addRepresentation("cartoon",
    param = list(color = colorByValue(c("A:10" = 1, "A:20" = 2, "A:30" = 3))))

if (interactive()) {
  library(shiny)
  ui <- fluidPage(
    sliderInput("k", "Score = sin(resno / k)", 1, 20, 5),
    NGLVieweROutput("structure")
  )
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("1CRN") %>%
        addRepresentation("cartoon", param = list(name = "cartoon"))
    })
    observeEvent(input$k, {
      residues <- input$structure_residues
      req(residues)
      residues$value <- sin(residues$resno / input$k)
      NGLVieweR_proxy("structure") %>%
        updateColor("cartoon", colorByValue(residues, domain = c(-1, 1)))
    })
  }
  shinyApp(ui, server)
}

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

magrittr

%>%

tools

file_ext()

Remove a selection

Description

Remove an existing NGLVieweR selection in Shinymode.

Usage

removeSelection(NGLVieweR_proxy, name)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• NGLVieweR_example() See example "removeSelection".

Other selections: addSelection(), updateSelection()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
     removeSelection("sel1")

## End(Not run)

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$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(name = "cartoon", colorScheme = "residueindex")
        )
    })
    observeEvent(input$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)
}

Set selection parameters

Description

Set selection parameters.

Usage

selectionParameters(NGLVieweR, proximity = 3, level = "residue")

Arguments

Value

Returns list of selection parameters to NGLVieweR htmlwidgets object.

Examples

NGLVieweR("7CID") %>%
 addRepresentation("cartoon") %>%
 selectionParameters(3, "residue")

# Shiny context
if (interactive()) {
   library(shiny)
   ui <- fluidPage(NGLVieweROutput("structure"))
   server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon") %>%
        selectionParameters(3, "residue")
    })
    observeEvent(input$structure_selAround, {
      NGLVieweR_proxy("structure") %>% removeSelection("selAround")
      NGLVieweR_proxy("structure") %>%
        addSelection(
          "ball+stick",
          param =
            list(
              name = "selAround",
              sele = input$structure_selAround,
              colorValue = "grey"
            )
        )
    })
  }
  shinyApp(ui, server)
}

Set Focus

Description

Set Focus

Usage

setFocus(NGLVieweR, focus = 0)

Arguments

Details

The focus sets the clipping planes and the fog (the NGL.js stage parameters clipNear, clipFar, fogNear and fogFar). Without setFocus() the viewer uses the NGL.js defaults (with the default clipScale = "relative" these equal focus 0). Values of these four parameters given in stageParameters() win over setFocus().

Value

setFocus parameter in NGLVieweR htmlwidgets object.

See Also

updateFocus()

Other options: setQuality(), snapShot(), updateFocus(), updateFullscreen()

Examples

NGLVieweR("7CID") %>%
  addRepresentation("cartoon", 
  param=list(name="cartoon", colorValue="blue")) %>%
  setFocus(0)

Set Position

Description

Set position for the representation

Usage

setPosition(NGLVieweR, x = 0, y = 0, z = 0)

Arguments

Value

NGLVieweR object with updated setPosition parameters.

See Also

• setScale()

• zoomMove()

• setRotation()

Other transformations: setRotation(), setScale(), zoomMove()

Examples

NGLVieweR("7CID") %>%
stageParameters(backgroundColor = "white") %>%
addRepresentation("cartoon", param=list(name="cartoon", colorValue="red")) %>%
addRepresentation("ball+stick", param=list(name="ball+stick",
colorValue="yellow",
colorScheme="element",
sele="200")) %>%
setPosition(25, 0, 0)

Set Quality

Description

Set Quality

Usage

setQuality(NGLVieweR, quality = "medium")

Arguments

Details

Without setQuality() the viewer uses the NGL.js default ("medium"). A quality given in stageParameters() wins over setQuality().

Value

setQuality parameter in NGLVieweR htmlwidgets object.

See Also

Other options: setFocus(), snapShot(), updateFocus(), updateFullscreen()

Examples

NGLVieweR("7CID") %>%
  addRepresentation("cartoon",
  param=list(name="cartoon", colorValue="blue")) %>%
  setQuality("medium")

Set rock

Description

Set rock animation

Usage

setRock(NGLVieweR, rock = TRUE)

Arguments

Details

Only one animation can run at a time. If both setRock(TRUE) and setSpin(TRUE) are used, the structure spins.

Value

setRock parameter to TRUE or FALSE in NGLVieweR htmlwidgets object.

See Also

• setSpin()

• updateRock()

Other animations: setSpin(), updateRock(), updateSpin(), updateZoomMove()

Examples

NGLVieweR("7CID") %>%
 addRepresentation("cartoon", param=list(name="cartoon", colorValue="blue")) %>%
 setRock(TRUE)

Rotate View

Description

Set rotation for the representation

Usage

setRotation(NGLVieweR, x = 0, y = 0, z = 0, degrees = TRUE)

Arguments

Value

NGLVieweR object with updated rotateView parameters.

See Also

• setScale()

• zoomMove()

• setPosition()

Other transformations: setPosition(), setScale(), zoomMove()

Examples

NGLVieweR("7CID") %>%
stageParameters(backgroundColor = "white") %>%
addRepresentation("cartoon", param=list(name="cartoon", colorValue="red")) %>%
addRepresentation("ball+stick", param=list(name="ball+stick",
colorValue="yellow",
colorScheme="element",
sele="200")) %>%
setRotation(30, 45, 60, degrees = TRUE)

Set Scale

Description

Set the scale factor for the representation

Usage

setScale(NGLVieweR, scale = 1)

Arguments

Value

Updated NGLVieweR object with new scale parameter.

See Also

• zoomMove()

• setRotation()

• setPosition()

Other transformations: setPosition(), setRotation(), zoomMove()

Examples

NGLVieweR("7CID") %>%
addRepresentation("cartoon", 
param=list(name="cartoon", colorValue="blue")) %>%
setScale(2)

Set Spin

Description

Set Spin animation

Usage

setSpin(NGLVieweR, spin = TRUE)

Arguments

Details

Only one animation can run at a time. If both setSpin(TRUE) and setRock(TRUE) are used, the structure spins.

Value

setSpin parameter to TRUE or FALSE in NGLVieweR htmlwidgets object.

See Also

• setRock()

• updateSpin()

Other animations: setRock(), updateRock(), updateSpin(), updateZoomMove()

Examples

NGLVieweR("7CID") %>%
 addRepresentation("cartoon", param=list(name="cartoon", colorValue="blue")) %>%
 setSpin(TRUE)

Set superpose

Description

Enable or disable superposition of multiple structures, with options to specify the reference structure and selection strings for alignment.

Usage

setSuperpose(
  NGLVieweR,
  reference = 1,
  sele_reference,
  sele_target,
  superpose = TRUE
)

Arguments

Value

Sets the superpose list in the NGLVieweR htmlwidgets object.

Examples

NGLVieweR("1GZM") %>%
  addRepresentation("cartoon", param = list(color = "blue")) %>%
  addStructure("1U19") %>%
  addRepresentation("cartoon", param = list(color = "orange")) %>%
  setSuperpose(
    reference = 1, 
    sele_reference = ":A", 
    sele_target = ":A", 
    superpose = TRUE
  )

Snapshot

Description

Make a snapshot of a NGLVieweR object in Shinymode.

Usage

snapShot(NGLVieweR_proxy, fileName = "Snapshot", param = list())

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

NGLVieweR_example() See example "snapshot".

Other options: setFocus(), setQuality(), updateFocus(), updateFullscreen()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
snapShot("Snapshot", param = list(
                               antialias = TRUE,
                               trim = TRUE,
                               transparent = TRUE,
                               scale = 1))

## End(Not run)

if (interactive()) {
  library(shiny)

  ui <- fluidPage(
    titlePanel("Viewer with API inputs"),
    sidebarLayout(
      sidebarPanel(
        actionButton("snapshot", "Snapshot"),
      ),
      mainPanel(
        NGLVieweROutput("structure")
      )
    )
  )
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(
            name = "cartoon",
            color = "residueindex"
          )
        )
    })
    observeEvent(input$snapshot, {
      NGLVieweR_proxy("structure") %>%
        snapShot("Snapshot",
          param = list(
            antialias = TRUE,
            trim = TRUE,
            transparent = TRUE,
            scale = 1
          )
        )
    })
  }
  shinyApp(ui, server)
}

Set stage parameters

Description

Set stage parameters.

Usage

stageParameters(NGLVieweR, ...)

Arguments

Details

Options that are not given use the NGL.js defaults. In Shiny, this also holds when renderNGLVieweR() re-renders: an option set in an earlier render but not in the current one returns to its default.

setFocus() and setQuality() are shortcuts that set clipping, fog and quality. Options named here win over them: for example setFocus(50) %>% stageParameters(fogFar = 60) keeps the clipping of focus 50 with fogFar 60.

All NGL.js stage parameters can be set here or changed later with updateStage(). For example:

• Clipping: clipNear, clipFar, clipDist, clipMode ("scene" or "camera") and clipScale ("relative" or "absolute").

• Fog: fogNear and fogFar.

• Lighting: lightColor, lightIntensity, ambientColor and ambientIntensity.

• Camera: cameraType ("perspective", "orthographic" or "stereo"), cameraFov and cameraEyeSep.

• Mouse controls: mousePreset ("default", "pymol", "coot" or "astexviewer").

Value

Returns list of stage parameters to NGLVieweR htmlwidgets object.

See Also

• updateStage()

• NGLVieweR_example() See example "basic".

Examples

NGLVieweR("7CID") %>%
 stageParameters(backgroundColor = "white", zoomSpeed = 1) %>%
 addRepresentation("cartoon", param = list(name = "cartoon", colorScheme="residueindex"))

# Orthographic camera, PyMOL mouse controls and fog
NGLVieweR("7CID") %>%
  stageParameters(
    cameraType = "orthographic",
    mousePreset = "pymol",
    fogNear = 40,
    fogFar = 80
  ) %>%
  addRepresentation("cartoon")

if (interactive()) {
  library(shiny)
  ui <- fluidPage(NGLVieweROutput("structure"))
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        stageParameters(backgroundColor = "white", zoomSpeed = 1) %>%
        addRepresentation("cartoon",
          param = list(name = "cartoon", colorScheme = "residueindex")
        )
    })
  }
  shinyApp(ui, server)
}

Update color of a selection

Description

Update color of an existing NGLVieweR selection in Shinymode.

Usage

updateColor(NGLVieweR_proxy, name, color)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• NGLVieweR_example() See example "updateColor".

Other updates: updateRepresentation(), updateStage(), updateVisibility()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
     updateColor("cartoon", "red")

## End(Not run)

if (interactive()) {
  library(shiny)
  library(colourpicker)

  ui <- fluidPage(
    titlePanel("Viewer with API inputs"),
    sidebarLayout(
      sidebarPanel(
        colourInput("color", "red", "red"),
        actionButton("update", "Update"),
      ),
      mainPanel(
        NGLVieweROutput("structure")
      )
    )
  )
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(name = "cartoon", color = "residueindex")
        )
    })
    observeEvent(input$update, {
      NGLVieweR_proxy("structure") %>%
        updateColor("cartoon", isolate(input$color))
    })
  }
  shinyApp(ui, server)
}

Update Focus

Description

Update the focus of an existing NGLVieweR object in Shinymode.

Usage

updateFocus(NGLVieweR_proxy, focus = 0)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• setFocus()

• NGLVieweR_example() See example "updateFocus".

Other options: setFocus(), setQuality(), snapShot(), updateFullscreen()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
  updateFocus(focus = 50)

## End(Not run)

if (interactive()) {
  library(shiny)
  ui = fluidPage(
    titlePanel("Viewer with API inputs"),
    sidebarLayout(
      sidebarPanel(
        sliderInput("focus", "Focus", 0, 100, 50)
      ),
      mainPanel(
        NGLVieweROutput("structure")
      )
    )
  )
  server = function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
        param = list(name = "cartoon", color= "red"))
    })
    observeEvent(input$focus, {
      NGLVieweR_proxy("structure") %>%
        updateFocus(input$focus)
    })
  }
shinyApp(ui, server)
}

Fullscreen

Description

Enter or leave fullscreen. Works in Shinymode.

Usage

updateFullscreen(
  NGLVieweR_proxy,
  fullscreen = TRUE,
  element = c("page", "viewer")
)

Arguments

Details

Browsers only allow entering fullscreen in response to a user action, such as clicking a button that triggers updateFullscreen().

Value

API call containing NGLVieweR id and list of message parameters.

See Also

NGLVieweR_example() See example "updateFullscreen".

Other options: setFocus(), setQuality(), snapShot(), updateFocus()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>% updateFullscreen()

## End(Not run)

if (interactive()) {
library(shiny)

ui <- fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      actionButton("enter", "Enter fullscreen"),
      actionButton("exit", "Exit fullscreen")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
 output$structure <- renderNGLVieweR({
  NGLVieweR("7CID") %>%
    addRepresentation("cartoon",
      param = list(name = "cartoon", color = "red")
    )
})

  observeEvent(input$enter, {
  NGLVieweR_proxy("structure") %>%
    updateFullscreen(TRUE)
})

  observeEvent(input$exit, {
  NGLVieweR_proxy("structure") %>%
    updateFullscreen(FALSE)
})
}
  shinyApp(ui, server)
}

Update Representation

Description

Update an existing NGLVieweR representation in Shinymode.

Usage

updateRepresentation(NGLVieweR_proxy, name, param = list())

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• addSelection() Add a new selection to a NGLVieweR object.

• addRepresentation()

• NGLVieweR_example() See example "updateRepresentation".

Other updates: updateColor(), updateStage(), updateVisibility()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
  updateRepresentation("cartoon",
    param = list(
      name = "cartoon",
      color = isolate(input$color),
      opacity = isolate(input$opacity)
    )
  )

## End(Not run)

if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      selectInput("color", "Color", c("red", "white", "blue")),
      sliderInput("opacity", "Opacity", 0, 1, 1),
      actionButton("update", "Update"),
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
                        param = list(name = "cartoon", color="red"))
  })
observeEvent(input$update, {
  NGLVieweR_proxy("structure") %>%
    updateRepresentation("cartoon",
      param = list(
        color = isolate(input$color),
        opacity = isolate(input$opacity)
      )
    )
})
 }
shinyApp(ui, server)
}

Update Rock

Description

Start rock animation and stop spinning. Works on an existing NGLVieweR object in Shinymode.

Usage

updateRock(NGLVieweR_proxy, rock = TRUE)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• setRock()

• NGLVieweR_example() See example "updateAnimation".

Other animations: setRock(), setSpin(), updateSpin(), updateZoomMove()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>% updateRock(TRUE)

## End(Not run)

if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      radioButtons("animate", label = "Animation",
      choices = c("None", "Spin", "Rock"), selected = "None")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
      param = list(name = "cartoon", color="red"))
  })

  observeEvent(input$animate,{
    if(input$animate == "Rock"){
      NGLVieweR_proxy("structure") %>%
      updateRock(TRUE)
    } else if(input$animate == "Spin") {
      NGLVieweR_proxy("structure") %>%
      updateSpin(TRUE)
    } else{
      NGLVieweR_proxy("structure") %>%
      updateRock(FALSE) %>%
      updateSpin(FALSE)
    }
  })
 }
shinyApp(ui, server)
}

Update a selection

Description

Update the selected residues of an existing NGLVieweR selection in Shinymode.

Usage

updateSelection(NGLVieweR_proxy, name, sele = "none")

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• NGLVieweR_example() See example "updateSelection".

Other selections: addSelection(), removeSelection()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
  updateSelection("ball+stick", sele = "1-20")

## End(Not run)

if (interactive()) {
  library(shiny)
  ui <- fluidPage(
    titlePanel("Viewer with API inputs"),
    sidebarLayout(
      sidebarPanel(
        textInput("selection", "Selection", "1-20"),
        actionButton("update", "Update")
      ),
      mainPanel(
        NGLVieweROutput("structure")
      )
    )
  )
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(name = "cartoon", color = "red")
        ) %>%
        addRepresentation("ball+stick",
          param = list(
            name = "ball+stick",
            colorValue = "yellow",
            colorScheme = "element",
            sele = "1-20"
          )
        )
    })
    observeEvent(input$update, {
      NGLVieweR_proxy("structure") %>%
        updateSelection("ball+stick", sele = isolate(input$selection))
    })
  }
  shinyApp(ui, server)
}

Update Spin

Description

Start spin animation and stop rocking. Works on an existing NGLVieweR object in Shinymode.

Usage

updateSpin(NGLVieweR_proxy, spin = TRUE)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• setSpin()

• NGLVieweR_example() See example "updateAnimation".

Other animations: setRock(), setSpin(), updateRock(), updateZoomMove()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>% updateRock(TRUE)

## End(Not run)
if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      radioButtons("animate", label = "Animation",
                   choices = c("None", "Spin", "Rock"), selected = "None")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
      param = list(name = "cartoon", color="red"))
  })

  observeEvent(input$animate,{
    if(input$animate == "Rock"){
      NGLVieweR_proxy("structure") %>%
       updateRock(TRUE)
    } else if(input$animate == "Spin") {
      NGLVieweR_proxy("structure") %>%
       updateSpin(TRUE)
    } else{
      NGLVieweR_proxy("structure") %>%
       updateRock(FALSE) %>%
       updateSpin(FALSE)
    }
  })
 }
shinyApp(ui, server)
}

Update Stage

Description

Update an existing NGLVieweR stage in Shinymode.

Usage

updateStage(NGLVieweR_proxy, param = list())

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• stageParameters()

• NGLVieweR_example() See example "updateStage".

Other updates: updateColor(), updateRepresentation(), updateVisibility()

Examples

## Not run: 
NGLVieweR("7CID") %>%
 addRepresentation("cartoon",
                   param = list(name = "cartoon", color="red")) %>%
 stageParameters(backgroundColor = "black")

## End(Not run)

if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      selectInput("background", "Background", c("black", "white", "blue")),
      actionButton("update", "Update"),
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server <- function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", color = "red")
      ) %>%
      stageParameters(backgroundColor = "black")
  })
  observeEvent(input$update, {
    NGLVieweR_proxy("structure") %>%
      updateStage(
      param = list("backgroundColor" = isolate(input$background)))
  })
}
shinyApp(ui, server)
}

Update visibility

Description

Hide or show an existing NGLVieweR selection in Shinymode.

Usage

updateVisibility(NGLVieweR_proxy, name, value = FALSE)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

NGLVieweR_example() See example "updateVisibility".

Other updates: updateColor(), updateRepresentation(), updateStage()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>%
 updateVisibility("cartoon", value = TRUE)

## End(Not run)

if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      actionButton("show", "Show"),
      actionButton("hide", "Hide"),
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
                        param = list(name = "cartoon", color="residueindex"))
  })
  observeEvent(input$show, {
    NGLVieweR_proxy("structure") %>%
      updateVisibility("cartoon", value = TRUE)

  })
  observeEvent(input$hide, {
    NGLVieweR_proxy("structure") %>%
      updateVisibility("cartoon", value = FALSE)

  })
}
shinyApp(ui, server)
}

Update zoomMove

Description

Add a zoom animation on an existing NGLVieweR object.

Usage

updateZoomMove(
  NGLVieweR_proxy,
  center,
  zoom,
  duration = 0,
  z_offSet = 0,
  structureIndex = NULL,
  structure = NULL
)

Arguments

Value

API call containing NGLVieweR id and list of message parameters.

See Also

• zoomMove()

• NGLVieweR_example() See example "updateZoomMove".

Other animations: setRock(), setSpin(), updateRock(), updateSpin()

Examples

## Not run: 
NGLVieweR_proxy("structure") %>% updateZoomMove(center = "200",
                                               zoom = "200",
                                               z_offSet = 80,
                                               duration = 2000)

## End(Not run)

if (interactive()) {
library(shiny)

ui = fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      textInput("center", "Center", "200"),
      textInput("zoom", "Zoom", "200"),
      numericInput("zoomOffset", "Zoom offset", 80,0,100),
      numericInput("duration", "Duration", 2000,0,2000),
      actionButton("zoom", "Zoom"),
      actionButton("reset", "Reset")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
      param = list(name = "cartoon", color="red")) %>%
      addRepresentation("ball+stick",
      param = list(name = "ball+stick", sele="200"))
  })

observeEvent(input$zoom, {
  NGLVieweR_proxy("structure") %>%
    updateZoomMove(
      center = isolate(input$center),
      zoom = isolate(input$zoom),
      z_offSet = isolate(input$zoomOffset),
      duration = isolate(input$duration)
    )
})

observeEvent(input$reset, {
  NGLVieweR_proxy("structure") %>%
    updateZoomMove(
      center = "*",
      zoom = "*",
      z_offSet = 0,
      duration = 1000
    )
})
}
shinyApp(ui, server)
}

Set zoomMove

Description

Add a zoom animation

Usage

zoomMove(NGLVieweR, center, zoom, duration = 0, z_offSet = 0)

Arguments

Details

Applies to the last structure added. The camera moves after all structures are loaded and superposed (see setSuperpose()). If zoomMove() is used for several structures, the last one is used (with a warning). The center is that of the atom coordinates, so it does not follow setPosition(), setRotation() or setScale().

Value

List of zoomMove parameters to NGLVieweR htmlwidgets object.

See Also

• setScale()

• setRotation()

• setPosition()

Other transformations: setPosition(), setRotation(), setScale()

Examples

NGLVieweR("7CID") %>%
stageParameters(backgroundColor = "white") %>%
  addRepresentation("cartoon", param=list(name="cartoon", colorValue="red")) %>%
  addRepresentation("ball+stick", param=list(name="ball+stick",
                                             colorValue="yellow",
                                             colorScheme="element",
                                             sele="200")) %>%
  zoomMove("200:A.C", "200:A.C", 2000, -20)