Description
visNetMul is supposed to visualise the same graph but with
multiple colorings according to input data matrix
Usage
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",
...)
Arguments
- g
- an object of class "igraph" or "graphNEL"
- data
- 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)
- height
- a numeric value specifying the height of device
- margin
- margins as units of length 4 or 1
- border.color
- the border color of each figure
- colormap
- 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
http://html-color-codes.info/color-names
- ncolors
- the number of colors specified over the colormap
- zlim
- 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
- colorbar
- logical to indicate whether to append a colorbar. If
pattern is null, it always sets to false
- colorbar.fraction
- the relative fraction of colorbar block
against the figure block
- newpage
- logical to indicate whether to open a new page. By
default, it sets to true for opening a new page
- glayout
- 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.auto", "layout.random", "layout.circle", "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
http://igraph.org/r/doc/layout_nicely.html
- mtext.side
- on which side of the mtext plot (1=bottom, 2=left,
3=top, 4=right)
- mtext.adj
- the adjustment for mtext alignment (0 for left or
bottom alignment, 1 for right or top alignment)
- mtext.cex
- the font size of mtext labels
- mtext.font
- the font weight of mtext labels
- mtext.col
- the color of mtext labels
- ...
- additional graphic parameters. See
http://igraph.org/r/doc/plot.common.html for the complete list.
Value
invisible
Note
none
Examples
# 1) generate a random graph according to the ER model
g <- erdos.renyi.game(100, 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)