Function to visualise the same graph but with multiple graph node colorings according to input data matrix


visNetMul is supposed to visualise the same graph but with multiple colorings according to input data matrix


visNetMul(g, data, height = 7, margin = rep(0.1, 4), border.color = "#EEEEEE", colormap = c("bwr", 
  "jet", "gbr", "wyr", "br", "yr", "rainbow", "wb"), ncolors = 40, zlim = NULL, 
      colorbar = T, colorbar.fraction = 0.25, newpage = T, glayout = layout.fruchterman.reingold, 
      mtext.side = 3, mtext.adj = 0, mtext.cex = 1, mtext.font = 2, mtext.col = "black", 


an object of class "igraph" or "graphNEL"
an input data matrix used to color-code vertices/nodes. One column corresponds to one graph node coloring. The input matrix must have row names, and these names should include all node names of input graph, i.e. V(g)$name, since there is a mapping operation. After mapping, the length of the patern vector should be the same as the number of nodes of input graph. The way of how to color-code is to map values in the pattern onto the whole colormap (see the next arguments: colormap, ncolors, zlim and colorbar)
a numeric value specifying the height of device
margins as units of length 4 or 1
the border color of each figure
short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in
the number of colors specified over the colormap
the minimum and maximum z/patttern values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted
logical to indicate whether to append a colorbar. If pattern is null, it always sets to false
the relative fraction of colorbar block against the figure block
logical to indicate whether to open a new page. By default, it sets to true for opening a new page
either a function or a numeric matrix configuring how the vertices will be placed on the plot. If layout is a function, this function will be called with the graph as the single parameter to determine the actual coordinates. This function can be one of "", "layout.random", "", "layout.sphere", "layout.fruchterman.reingold", "layout.kamada.kawai", "layout.spring", "layout.reingold.tilford", "layout.fruchterman.reingold.grid", "layout.lgl", "layout.graphopt", "layout.svd" and "layout.norm". A full explanation of these layouts can be found in
on which side of the mtext plot (1=bottom, 2=left, 3=top, 4=right)
the adjustment for mtext alignment (0 for left or bottom alignment, 1 for right or top alignment)
the font size of mtext labels
the font weight of mtext labels
the color of mtext labels
additional graphic parameters. See for the complete list.






# 1) generate a random graph according to the ER model g <-, 1/80) # 2) produce the induced subgraph only based on the nodes in query subg <- dNetInduce(g, V(g), knn=0) # 3) visualise the module with vertices being color-coded by scores nnodes <- vcount(subg) nsamples <- 10 data <- matrix(runif(nnodes*nsamples), nrow=nnodes, ncol=nsamples) rownames(data) <- V(subg)$name visNetMul(g=subg, colormap="bwr", data=data, glayout=layout.fruchterman.reingold)

Source code


Source man

visNetMul.Rd visNetMul.pdf

See also

visNet, visNetAnimate