Layout

Source: R/layouts.R

Set network layout options

layout(cytoscape, name = NULL, fit = TRUE, padding = 30,
  boundingBox = NULL, avoidOverlap = TRUE, avoidOverlapPadding = 10,
  nodeDimensionsIncludeLabels = FALSE, spacingFactor = NULL,
  condense = FALSE, rows = NULL, cols = NULL, position = NULL,
  sort = NULL, animate = FALSE, animationDuration = 500,
  animationEasing = NULL, animateFilter = NULL, ready = NULL,
  stop = NULL, transform = NULL, ...)

# S3 method for cytoscape
layout(cytoscape, name = NULL, fit = TRUE,
  padding = 30, boundingBox = NULL, avoidOverlap = TRUE,
  avoidOverlapPadding = 10, nodeDimensionsIncludeLabels = FALSE,
  spacingFactor = NULL, condense = FALSE, rows = NULL, cols = NULL,
  position = NULL, sort = NULL, animate = FALSE,
  animationDuration = 500, animationEasing = NULL,
  animateFilter = NULL, ready = NULL, stop = NULL,
  transform = NULL, ...)

Arguments

cytoscape

object
name

character option, must b one of:

  • null

  • random

  • preset

  • grid

  • circle

  • concentric

  • breadthfirst

  • cose
fit

boolean whether to fit the viewport to the graph
padding

integer pixels padding used on fit
boundingBox

= undefined, // constrain layout bounds; x1, y1, x2, y2 or x1, y1, w, h
avoidOverlap

boolean prevents node overlap, may overflow boundingBox if not enough space
avoidOverlapPadding

integer pixels extra spacing around nodes when avoidOverlap = true
nodeDimensionsIncludeLabels

= false, // Excludes the label when calculating node bounding boxes for the layout algorithm
spacingFactor

= undefined, // Applies a multiplicative factor (>0) to expand or compress the overall area that the nodes take up
condense

boolean, uses all available space on false, uses minimal space on true
rows

integer force num of rows in the grid
cols

integer force num of columns in the grid
position

js function( node ), // returns row, col for element
sort

js a sorting function to order the nodes; e.g. function(a, b) return a.data('weight') - b.data('weight')
animate

boolean whether to transition the node positions
animationDuration

integer duration of animation in ms if enabled
animationEasing

= undefined, // easing of animation if enabled
animateFilter

= function ( node, i ) return true; , // a function that determines whether the node should be animated. All nodes animated by default on animate enabled. Non-animated nodes are positioned immediately when the layout starts
ready

= undefined, // callback on layoutready
stop

= undefined, // callback on layoutstop
transform

= 'function (node, position ) return position; '
...

additional parameters passed to the layout object

Value

cytoscape object

Examples


df <- cytoscape::comtrade

nodes <- data.frame(id = unique(c(df$reporter, df$partner)))
edges <- df %>%
  dplyr::select(source = reporter,
                target = partner) %>%
  dplyr::mutate(id = paste(source, '_', target))

cytoscape(nodes = nodes, edges = edges) %>%
  cytoscape::layout(4)
#> Error in layout.cytoscape(., 4): name %in% c("null", "random", "preset", "grid", "circle", "concentric",  .... is not TRUE