layout.cytoscape: Layout

In mrjoh3/cytoscape: Create and Style Simple Network Charts

Description

Set network layout options

Usage

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 class '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)

mrjoh3/cytoscape documentation built on Nov. 14, 2020, 9:29 a.m.