Add representation

Add a representation and its parameters.

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.

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.

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)
}