netviewOptions: NetView Options
In esteinig/netview: Mutual k-Nearest-Neighbour Networks for Population Analysis

Description Usage Arguments Details Value

View source: R/netviewOptions.R

Generate options for NetView.

1	netviewOptions(...)

`mknnWeights`	Construct networks with weighted edges, using the distance value from the input matrix [ bool, TRUE ]
`mknnAlgorithm`	Algorithm for mutual nearest neighbour search [ str, "cover_tree" ]
`communityAlgorithms`	Algorithms for community detection analysis [ str vector, c("Walktrap", "Infomap", "Fast-Greedy") ]
`selectionTitle`	Title for community k-Plot in plotSelection() [ str, "Community k-Plot"]
`selectionPlot`	Configure x- and y-axis breaks and line width of k-Plot [ int vector, c(5, 20, 1) ]
`nodeID`	Name of column in metaData defining IDs [ str, "ID" ]
`nodeGroup`	Name of column in metaData defining sample groups [ str, "Group" ]
`nodeColour`	Name of column in metaData defining sample colours [ str, "Colour" ]
`d3.nodeSize`	Name of column in metaData defining node sizes for networkD3 [ str, "Size" ]
`d3.height`	Height of widget networkD3 [ numeric, NULL ]
`d3.width`	Width of widget networkD3 [ numeric, NULL ]
`d3.colourScale`	Colour scale to use for groups in networkD3 [ str, NULL ]
`d3.fontSize`	Font size for labels in networkD3 [ int, 7 ]
`d3.fontFamily`	Font family for labels in networkD3 [ str, "times" ]
`d3.linkDistance`	Edge distance for force-directed layout in networkD3 [ int, 50 ]
`d3.linkWidth`	JS function to determine edge width [ str, "function(d) return Math.sqrt(d.value); " ]
`d3.radiusCalculation`	JS expression to determine node radius [ str, "Math.sqrt(d.nodesize)+6" ]
`d3.charge`	Charge parameter for force-directed layout networkD3 [ int, -120 ]
`d3.linkColour`	Colour od edges for networkD3 [ str, "#666" ]
`d3.opacity`	Node opacity for networkD3 [ numeric, 0.8 ]
`d3.zoom`	Zoom for networkD3 [ bool, TRUE ]
`d3.legend`	Legend for networkD3, using Groups [ bool, FALSE ]
`d3.bounded`	Bounds for networkD3 [ bool, FALSE ]
`d3.opacityNoHover`	Opacity change when hovering in networkD3 [ numeric, 0 ]
`d3.clickAction`	JS function for clicking a node in networkD3 [ str, NULL ]
`d3.linkX`	Multiplier for link distance, use instead of specifiying JS function in d3.linkWidth [ numeric, 20 ]

For examples and tutorials, please see our GitHub Repository: https://github.com/esteinig/netview

Allowed community-detection algorithm names are "Walktrap", "Infomap", "Fast-Greedy", "Edge Betweenness", "Label Propagation", "Louvain" and "Leading Eigenvector"
Allowed mutual nearest neighbour search algorithms, as implemented in nng from package cccd are "cover_tree", "kd_tree", "CR", "brute"

List of options for NetView.

esteinig/netview documentation built on Feb. 8, 2022, 7:17 a.m.