R/plotPrettyGraph.R

In neuroconductor/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' Simple plotPrettyGraph function saves to png.
#'
#' PlotPrettyGraph given inputs from the makeGraph function.  adapted from
#' http://is-r.tumblr.com/.
#'
#' @param adjacencyMatrix igraph adjacencyMatrix
#' @param functionToPlot igraph node-level graph value e.g. degree,
#' page.rank, etc
#' @param pngfn filename for output png or to screen if NA
#' @param scaleText relative size of text to vertices
#' @param vertexSize cex size of vertices
#' @param figScale the figure will be of square size 2^figScale in pixels
#' @param layoutmode see gplot.layout in sna package
#' @param hueval controls the hue in hsv
#' @return no output
#' @author Avants BB, Christopher DeSante and David Sparks
#' @examples
#'
#' data("bold_correlation_matrix",package="ANTsR")
#' dmat<-data.matrix(bold_correlation_matrix)
#' if ( usePkg("igraph") ) {
#'  gg<-makeGraph( dmat, 0.1 )
#'  rownames(gg$adjacencyMatrix)<-colnames(bold_correlation_matrix)
#'  plotPrettyGraph( gg$adjacencyMatrix, gg$degree , figScale=12 , scaleText=5 )
#'  }
#'
#' @export plotPrettyGraph
plotPrettyGraph <- function(  adjacencyMatrix, functionToPlot,
                              pngfn=tempfile(fileext = ".png"), scaleText=0.5, vertexSize = NA, figScale=11 ,
                              layoutmode = "eigen", hueval = 0 ) {
  # adapted from http://is-r.tumblr.com/
  if ( !usePkg("igraph") ) { print("Need igraph package"); return(NULL) }
  if ( !usePkg("sna") ) { print("Need sna package"); return(NULL) }
  as.matrix(sort(functionToPlot))
  # Now, to make the prettiest graph we can:
  if ( !is.na( pngfn ) )
    png( pngfn , height = 2^figScale, width = 2^figScale )
  par(mai = c(0, 0, 0, 0))
  frange<-(functionToPlot - min(functionToPlot)) /
    (max(functionToPlot) - min(functionToPlot))
  alpharange<-( frange*2 )
  alpharange[ alpharange > 1 ]<-1
  functionToPlotColor <- hsv( hueval , 1, frange, alpha=alpharange )
  functionToPlotScaler <- abs(functionToPlot)/max(abs(functionToPlot)) * 0.5 + 1/2
  if ( is.na( vertexSize ) ) vertexSize <- functionToPlotScaler
  # gplot is from sna
  prettyPlot <- sna::gplot(dat = adjacencyMatrix,
                           label = rownames(adjacencyMatrix),
                           mode = layoutmode,
                           pad = 0,
                           label.pad = 1,
                           boxed.labels = TRUE,
                           label.pos = 1,  # Below vertex
                           label.bg = "#ffffff99",
                           vertex.cex=vertexSize, # size of vertex
                           vertex.sides = 100,  # Basically circular
                           arrowhead.cex = functionToPlotScaler,
                           label.cex = functionToPlotScaler*scaleText,
                           edge.col = "#00000011",  # To make translucent bounding box
                           label.col = functionToPlotColor,
                           vertex.col = functionToPlotColor,
                           label.border = "#ffffff00",  # To hide borders
                           vertex.border = "#ffffff00" )  # To hide borders
  if ( !is.na( pngfn ) ) dev.off()
  detach('package:sna',unload=TRUE)
  if (!is.na(pngfn)) {
    return(pngfn)
  } else { 
    return(invisible(NULL))
  }
}