Title: Interactive 3D Visualization of Molecular Structures
Version: 1.4.0
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Description: Provides an 'htmlwidgets' https://www.htmlwidgets.org/ interface to 'NGL.js' http://nglviewer.org/ngl/api/. 'NGLvieweR' can be used to visualize and interact with protein databank ('PDB') and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation in Shiny.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: htmlwidgets, magrittr, tools, shiny
Suggests: knitr, webshot, markdown, rmarkdown, colourpicker
VignetteBuilder: knitr
URL: https://github.com/nvelden/NGLVieweR
BugReports: https://github.com/nvelden/NGLVieweR/issues
NeedsCompilation: no
Packaged: 2024-11-22 18:57:06 UTC; nielsvandervelden
Author: Niels van der Velden [aut, cre], Alexander Rose [cph] (NGL.js library)
Repository: CRAN
Date/Publication: 2024-11-22 19:10:02 UTC

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

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

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

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)
}

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)
}

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")
}

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

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)

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

(optional) The index of the specific structure to which the selection should be added (index 0 for the first). If not specified, the selection will be applied to all loaded structures.

Value

API call containing NGLVieweR id and list of message parameters.

See Also

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. Can be a PDB entry code (e.g. "7CID"), a file path to a structure file, or a text representation of the structure.

format

Format of the structure file, if reading from a file. Supported formats are "pdb", "cif", etc. If the file format cannot be inferred from the file name, this parameter must be specified.

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.

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

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

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

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.

Value

setRock parameter to TRUE or FALSE in NGLVieweR htmlwidgets object.

See Also

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

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

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

Value

setSpin parameter to TRUE or FALSE in NGLVieweR htmlwidgets object.

See Also

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).

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.

Value

Returns list of stage parameters to NGLVieweR htmlwidgets object.

See Also

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

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

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

Put viewer in fullscreen. Works in Shinymode.

Usage

updateFullscreen(NGLVieweR_proxy, fullscreen = TRUE)

Arguments

NGLVieweR_proxy

A NGLVieweR object.

fullscreen

If TRUE put viewer in fullscreen.

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("fullscreen", "Fullscreen"),
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server = function(input, output) {
 output$structure <- renderNGLVieweR({
  NGLVieweR("7CID") %>%
    addRepresentation("cartoon",
      param = list(name = "cartoon", color = "red")
    )
})

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

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

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

Usage

updateSelection(NGLVieweR_proxy, name = 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

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

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

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
)

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

Optional index of the structure to target for the zoom animation. If NULL (default), the first structure (index 0) is targeted.

Value

API call containing NGLVieweR id and list of message parameters.

See Also

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).

Value

List of zoomMove parameters to NGLVieweR htmlwidgets object.

See Also

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)