R/mgp.R

In ECGen/ComGenR: Functions for COMmunity GENetics analyses in R

#' Modified graph plotting for network models.
#' 
#' High level access to the gplot function in the sna package.
#' 
#' This is a high level function for plotting networks using the sna package
#' specifically tailored for community data based network models.
#' 
#' @param net A network.
#' @param com The community matrix used to generate the network with species in
#' the same order as the network.
#' @param my.coord A set of point coordinates to coordinates the nodes in the
#' network.
#' @param loc Logical: should the location (i.e. coordinates) of the plotted
#' nodes be returned?
#' @param v.scale Value to scale the node (i.e. vertex) size.
#' @param v.min Minumum size for a node (i.e. vertex).
#' @return %% ~Describe the value returned %% If it is a LIST, use %%
#' @export mgp
#' @note %% ~~further notes~~
#' @author Matthew K. Lau 
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#' 
#' ##---- Should be DIRECTLY executable !! ----
#' ##-- ==>  Define data, use random,
#' ##--	or do  help(data=index)  for the standard data sets.
#' 
mgp <- function(net = 'species network', com = 'community matrix',
                my.coord = '', loc = TRUE, v.scale = 3, v.min = 0.1,
                displaylabels=FALSE){
v.cex <- apply(com[,apply(com,2,sum)!=0],2,sum) #scaling node size by the log of species frequencies
v.cex <- (((v.cex/sum(v.cex))/max((v.cex/sum(v.cex))))*v.scale)+v.min
e.col <- net
e.col[net>0.5] <- 'red'
e.col[net<0.5] <- 'black'
e.col[net==0.5] <- 'grey'

if (length(my.coord)==1){
  coord <- gplot(abs(net),displaylabels=displaylabels,gmode='graph',pad=1.5,
        edge.lwd=(abs(net)),vertex.cex=v.cex,vertex.col='grey',
        edge.col=e.col,label.lty=1)
}else{
  gplot(abs(net),displaylabels=displaylabels,gmode='graph',pad=1.5,
        edge.lwd=(abs(net)),vertex.cex=v.cex,vertex.col='grey',
        edge.col=e.col,coord=my.coord,label.lty=1)
}
if (loc){return(coord)}else{}
}