Package 'NGLVieweR'

Add representation

Description

Add a representation and its parameters.

Usage

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

Arguments

NGLVieweR	A NGLVieweR object.
type	Type of representation. Most common options are "cartoon", "ball+stick", "line", "surface", "ribbon" and "label". For a full list of options, see the "structureRepresentation" method in the official NGL.js manual.
param	Options for the different types of representations. Most common options are name, opacity, colorScheme, sele, colorValue and visibility. For a full list of options, see the general "RepresentationParameters" method and type specific Label-, Structure- and Surface- RepresentationParameters in the official NGL.js manual.

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"
    )
  )

# 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

NGLVieweR_proxy	A NGLVieweR object.
type	Type of representation. Most common options are "cartoon", "ball+stick", "surface", "ribbon" and "label".
param	Options for the different types of representations. Most common options are name, opacity, colorScheme, sele, colorValue and visibility. For a full list of options, see the general "RepresentationParameters" method and type specific Label-, Structure- and Surface- RepresentationParameters in the official NGL.js manual.
structureIndex	Deprecated; use structure. The same, but counting from 0.
structure	(optional) Number of the structure to add the selection to, counting from 1 in the order the structures were added (see addStructure()). In Shiny, input$<outputId>_selectionStructure gives the number of the last clicked structure. If not specified, the selection is added to all loaded structures.

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

NGLVieweR	A NGLVieweR object.
data	Structure data to be added, in the same forms as in NGLVieweR(): a PDB entry code (e.g. "7CID"), a file path (also compressed with gzip, bzip2 or xz), or the file contents as a single string or a vector of lines.
format	Format of the structure, as in NGLVieweR() (e.g. "pdb", "cif"). Needed for file contents and when the format cannot be inferred from the file name.

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.

---

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

data	A PDB entry code (e.g. "7CID"), the path to a structure file, or the file contents as a single string or a vector of lines (e.g. from readLines()). Files compressed with gzip, bzip2 or xz (.gz, .bz2, .xz) are decompressed.
format	Input format (cif, mmcif, mcif, pdb, ent, pqr, gro, sdf, sd, mol2), with or without a leading dot. Needed for file contents and for files without a recognisable extension. Binary formats such as MMTF are not supported.
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

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 = "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)
}

---

Run NGLVieweR example Shiny app

Description

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

Usage

NGLVieweR_example(example = "basic")

Arguments

example

Example type for which to see an example, possible values are: "basic", "API", "addSelection", "removeSelection", "snapshot", "updateAnimation", "updateColor", "updateFocus", "updateFullscreen", "updateRepresentation", "updateSelection", "updateStage", "updateVisibility", "updateZoomMove", "multiStructureSelection".

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")
}

---

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

outputId	output variable to read from
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.
expr	An expression that generates a NGLVieweR.
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.
id	single-element character vector indicating the output ID of the chart to modify (if invoked from a Shiny module, the namespace will be added automatically)
session	The Shiny session object to which the map belongs; usually the default value will suffice.

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

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

---

Remove a selection

Description

Remove an existing NGLVieweR selection in Shinymode.

Usage

removeSelection(NGLVieweR_proxy, name)

Arguments

NGLVieweR_proxy	A NGLVieweR object.
name	Name of selection to be removed.

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

NGLVieweR	A NGLVieweR object.
proximity	Set distance in angstrom for atoms to return in proximity of selection. Default = 3.
level	Set level on which atoms in proximity of selection are returned. Options are "residue" (default) or atom".

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

NGLVieweR	A NGLVieweR object.
focus	Set focus between 0 (default) to 100.

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

NGLVieweR	A NGLVieweR object.
x	Position along the x-axis in angstroms. Default is 0.
y	Position along the y-axis in angstroms. Default is 0.
z	Position along the z-axis in angstroms. Default is 0.

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

NGLVieweR	A NGLVieweR object.
quality	Set rendering quality. Can be "low", "medium" (default) or "high".

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

NGLVieweR	A NGLVieweR object.
rock	If TRUE (default), start rocking and stop spinning.

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

NGLVieweR	A NGLVieweR object.
x	Rotation angle around the x-axis. Default is 0.
y	Rotation angle around the y-axis. Default is 0.
z	Rotation angle around the z-axis. Default is 0.
degrees	A logical value. If TRUE (default), the input angles are assumed to be in degrees and will be converted to radians. If FALSE, the angles are assumed to be in radians.

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

NGLVieweR	A NGLVieweR object.
scale	A numeric value indicating the scale factor (default is 1).

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

NGLVieweR	A NGLVieweR object.
spin	If TRUE (default), start spinning and stop rocking

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

NGLVieweR	A NGLVieweR object.
reference	The index of the reference structure to align other structures to. Defaults to 1 (the first loaded structure). The reference keeps its coordinates; every other structure is moved onto it.
sele_reference	Selection string for the reference structure, specifying which parts to align. Mandatory.
sele_target	Selection string for each target structure, specifying which parts to align. Mandatory.
superpose	Logical; if TRUE (default), enable superposition of multiple structures. Set to FALSE to disable.

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

NGLVieweR_proxy	A NGLVieweR object.
fileName	Optional name for Snapshot (default = "Snapshot").
param	Of type list, can be; antialias TRUE/FALSE, trim TRUE/FALSE, transparent TRUE/FALSE or scale numeric. For a full list of options, see "makeImage" and "ImageParameters" in the official NGL.js manual.

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

NGLVieweR	A NGLVieweR object.
...	Options controlling the stage. Most common options are backgroundColor, rotateSpeed, zoomSpeed, hoverTimeout and lightIntensity. For a full list of options, see the "stageParameters" method in the official NGL.js manual.

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.

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"))

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

NGLVieweR_proxy	A NGLVieweR object.
name	Name of selection to alter the color.
color	Can be a colorValue (color name or HEX code) or colorScheme (e.g. "element", "resname", "random" or "residueindex"). For a full list of options, see the "Colormaker" section in the official NGL.js manual.

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

NGLVieweR_proxy	A NGLVieweR object.
focus	Numeric value between 0-100 (default = 0).

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

NGLVieweR_proxy	A NGLVieweR object.
fullscreen	If TRUE (default) enter fullscreen, if FALSE leave it. Nothing happens if the page is already in the requested state.
element	What to show fullscreen: "page" (default) the whole page, so the app's own controls stay visible, or "viewer" only the viewer. Only used when entering fullscreen; users can always leave with Esc.

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

NGLVieweR_proxy	A NGLVieweR object.
name	Name of representation to alter the color.
param	Options for the different types of representations. Most common options are name, opacity, colorScheme, colorValue and visibility. For a full list of options, see the general "RepresentationParameters" method and type specific Label-, Structure- and Surface- RepresentationParameters in the official NGL.js manual.

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

NGLVieweR_proxy	A NGLVieweR object.
rock	If TRUE (default), start rocking and stop spinning.

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

NGLVieweR_proxy	A NGLVieweR object.
name	Name of selection.
sele	Selected atoms/residues. See the section "selection-language" in the official NGL.js manual.

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

NGLVieweR_proxy	A NGLVieweR object.
spin	If TRUE (default), start spinning and stop rocking.

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

NGLVieweR_proxy	A NGLVieweR object.
param	Of type list. Most common options are backgroundColor, rotateSpeed, zoomSpeed, hoverTimeout and lightIntensity. For a full list of options, see the "StageParameters" method in the official NGL.js manual.

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

NGLVieweR_proxy	A NGLVieweR object.
name	Name of selection to alter the color.
value	Hide FALSE or show TRUE selection. For a full description see "setVisibility" in the official NGL.js manual.

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

NGLVieweR_proxy	A NGLVieweR object.
center	Target distance of selected atoms/residues. See the section "selection-language" in the official NGL.js manual.
zoom	Target zoom of selected atoms/residues. See the section "selection-language" in the official NGL.js manual.
duration	Optional animation time in milliseconds (default = 0).
z_offSet	Optional zoom offset value (default = 0).
structureIndex	Deprecated; use structure. The same, but counting from 0.
structure	Optional number of the structure to zoom to, counting from 1 in the order the structures were added (see addStructure()). In Shiny, input$<outputId>_selectionStructure gives the number of the last clicked structure. If NULL (default), the first structure.

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

NGLVieweR	A NGLVieweR object.
center	Target distance of selected atoms/residues. See the section "selection-language" in the official NGL.js manual.
zoom	Target zoom of selected atoms/residues. See the section "selection-language" in the official NGL.js manual.
duration	Optional animation time in milliseconds (default = 0).
z_offSet	Optional zoom offset value (default = 0).

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)

---