plotGraphNELD3: Dynamic plot of a graph
In simPATHy: A Method for Simulating Data from Perturbed Biological Pathways

Description Usage Arguments Details Value References Examples

View source: R/graphic_function.R

Dynamic plot of a graphNEL object with the possibility to emphasize the strength of relations between nodes, represented by either a pairwise correlation or a partial correlation coefficient.

The interactive graph is an implementation of the javascript D3.js package (force-layout) for undirected and directed graphNEL objects (see references).

plotGraphNELD3(
  graph,
  type = "cor",
  S1 = NULL,
  S2 = NULL,
  colLim = c(-1, 1),
  legendColor = TRUE,
  colNode = "#c0c0c0"
)

`graph`	A graphNEL object.
`type`	Character string specifying which matrix is to be used. Either cor for correlation matrix, or pcor for partial correlation matrix.
`S1, S2`	Sample covariance matrix. If `S1` is supplied edges between nodes are colored in accordance with pairwise correlation or partial correlation coefficients. If `S2` supplied, the difference between the two corresponding correlation or partial correlation matrices is plotted.
`colLim`	Numeric vector of length two specifying the lower and upper bound of the color range (see Details).
`legendColor`	ogical value indicating whether the color legend should be added to the plot.
`colNode`	A character string specifying the colour of the nodes. The colour node is common for all nodes.

Admissible values for colLim are contained in the interval [-1,1] when S2=NULL, otherwise the admissible interval is [-2,2]. When an element is outside of the colLim interval, it is colored gray and represented as a dashed link.

Dynamic plot of a graphNEL object.

https://d3js.org (Micheal Bostock).

http://www.htmlwidgets.org (Ramnath Vaidyanathan, Kenton Russell, and RStudio).

https://christophergandrud.github.io/networkD3/ (Christopher Gandrud, JJ Allaire, & Kent Russell)

if(require(gRbase) & require(graph)){
  graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
  # Plot a graphNEL
  plotGraphNELD3(graph)

  # Plot a graphNEL coloring edges in correspondance with pairwise correlation coefficients
  S <- matrix(c(2,  0.8,0.5,-0.3,
                0.8,1.5,0.6,-0.7,
                0.5,0.6,1,  0.7,
                -0.3,-0.7,0.7,3), ncol=4,nrow=4)
  colnames(S) <- rownames(S) <- graph::nodes(graph)
  plotGraphNELD3(graph, S1=S)

  # Plot a graphNEL coloring edges in correspondance with partial correlation coefficients
  plotGraphNELD3(graph, S1=S, type="pcor")

  # Change the color range
  plotGraphNELD3(graph, S1=S, type="cor", colLim=c(-0.7,0.8))
  # Change nodes color
  plotGraphNELD3(graph, S1=S, type="cor", colNode = "pink")

  # Plot the difference between two graphical models
  S2 <- S
  S2[1,3] <- S2[3,1]<- -0.1
  plotGraphNELD3(graph,S1=S, S2=S2)

}