[Adephylo-commits] r4 - pkg/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 20 14:30:43 CET 2008
Author: jombart
Date: 2008-11-20 14:30:43 +0100 (Thu, 20 Nov 2008)
New Revision: 4
Added:
pkg/R/s.phylo4d.R
Log:
Added a s.phylo4d which is taken from my plot method for phylo4d in phylobase.
Added: pkg/R/s.phylo4d.R
===================================================================
--- pkg/R/s.phylo4d.R (rev 0)
+++ pkg/R/s.phylo4d.R 2008-11-20 13:30:43 UTC (rev 4)
@@ -0,0 +1,249 @@
+#############
+## s.phylo4d
+#############
+s.phylo4d <- function(x, treetype=c("phylogram","cladogram"), symbol=c("circles", "squares"),
+ center=TRUE, scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE,
+ show.tip.label=TRUE, show.node.label=TRUE, show.var.label=TRUE,
+ ratio.tree=1/3, font=3,
+ tip.label=x at tip.label, var.label=colnames(x at tip.data),
+ cex.symbol=1, cex.label=1, cex.legend=1, coord.legend=NULL, ...)
+{
+
+ ## preliminary stuff and checks
+ if (is.character(chk <- check_phylo4(x)))
+ stop("bad phylo4d object: ",chk)
+
+ if(!require(ape)) stop("the ape package is required")
+ if(cex.label<0.1) {
+ show.tip.label <- FALSE
+ show.node.label <- FALSE
+ show.var.label <- FALSE
+ }
+
+ cex <- par("cex")
+ symbol <- match.arg(symbol)
+ treetype <- match.arg(treetype)
+
+ SYMBSCALE <- 0.2 # i.e. max size of a plotted symbol is 0.2*cex.symbol inches
+
+ ## convert the tree into phylo
+ tre <- suppressWarnings(as(x,"phylo"))
+ tre$node.label <- x at node.label # this should be done by the as(x,"phylo")
+ ## plot only tree if no tip data
+ if(ncol(tdata(x,which="tip")) == 0) {
+ plot.phylo(tre, type=treetype, direction="rightwards", show.tip.label=show.tip.label,
+ show.node.label=show.node.label, cex=cex.label,
+ no.margin=FALSE, x.lim=NULL, y.lim=NULL, ...)
+ return(invisible())
+ }
+
+#### data handling
+ ## retrieve data
+ dat <- tdata(x, which="tip")
+ clas <- lapply(dat,class)
+ isNum <- sapply(clas, function(e) e %in% c("integer","numeric"))
+ ## keep only numeric data
+ dat <- dat[isNum]
+ var.label <- var.label[isNum]
+ ## order data like tips
+ E <- edges(x)
+ tips.ord <- E[,2][!E[,2] %in% E[,1]]
+ dat <- dat[tips.ord,,FALSE]
+ tip.label <- tip.label[tips.ord] # reorder tip labels
+ ## centring / scaling
+ dat <- as.data.frame(scale(dat,center=center,scale=scale))
+
+ ## compute bottom margin
+ ## ! use inches as units still these won't be changed by plot.phylo
+ temp <- var.label[which.max(nchar(var.label))] # longest tip label
+ lab.height <- strwidth(temp, units="inches", cex=cex.label) # height required by the longest var label
+ lab.height <- lab.height / par("pin")[1] # returned as a fraction of the plot region
+
+#### define plot region
+ plotreg <- plotreg0 <- par("plt")
+ plotreg.width <- plotreg0[2] - plotreg0[1]
+ plotreg.height <- plotreg0[4] - plotreg0[3]
+ plotreg[2] <- plotreg[1] + (ratio.tree)*plotreg.width # restrain the width for phylo
+ plotreg[3] <- plotreg[3] + plotreg.height*ifelse(show.var.label,lab.height+0.05,0.05) ## add internal vertical margins
+ plotreg[4] <- plotreg[4] - plotreg.height*0.05 # add internal vertical margins
+
+#### plot the tree
+ par(plt = plotreg)
+ plotres <- plot.phylo(tre, type=treetype, direction="rightwards", show.tip.label=FALSE,
+ show.node.label=show.node.label, cex=cex.label,
+ no.margin=FALSE, x.lim=NULL, y.lim=NULL, ...)
+
+#### plot the data
+ par(plt=plotreg0)
+ cur.usr.width <- par("usr")[2] - par("usr")[1] # beware: par("usr") does not adapt to the new plot region
+ usr.width <- cur.usr.width / ratio.tree
+ usr.height <- par("usr")[4] - par("usr")[3]
+
+ ## x.inset is the space between tree/data and data/tip.labels (in usr units)
+ x.inset <- SYMBSCALE * cex.symbol * usr.width / par("pin")[1]
+ y.inset <- SYMBSCALE * cex.symbol * usr.height / par("pin")[2]
+ x.base <- plotres$x.lim[2] + x.inset # start plotting from x.base rightwards
+ temp <- x at tip.label[which.max(nchar(x at tip.label))] # longest tip label
+ lab.width <- strwidth(temp, units="user", cex=cex.label) # compute the width to keep for tip labels
+ xrange.data <- c(x.base , (par("usr")[1]+usr.width) - lab.width - 2*x.inset) # plot data within this range
+
+ if(diff(xrange.data) < (x.inset*ncol(dat))) stop("No room left to plot data; please try reducing ratio.tree or cex.label.")
+
+ ## define x and y coordinates
+ x.grid <- seq(xrange.data[1],xrange.data[2], length=ncol(dat))
+ if(ncol(dat)==1) {x.grid <- mean(c(xrange.data[1],xrange.data[2]))}
+ y.grid <- seq(plotres$y.lim[1],plotres$y.lim[2],length=plotres$Ntip)
+ temp <- expand.grid(y.grid, x.grid) # here are coordinates for data
+ xy.data <- data.frame(x=temp[,2],y=temp[,1])
+
+ ## merge data and their coordinates
+ alldat <- cbind.data.frame(xy.data, unlist(dat))
+ ## fac <- factor(rep(1:ncol(dat), rep(nrow(dat),ncol(dat))))
+ ## alldat <- split(alldat, fac)
+
+ ## need to "reboot" the plot region without changing coordinates
+ ## seems that box does the job.
+ if(box) {box()} else {box(col="transparent")}
+ if(grid){
+ ## vertical segments
+ segments(x0=x.grid, y0=rep(min(y.grid),plotres$Ntip),
+ x1=x.grid, y1=rep(max(y.grid),plotres$Ntip), col="grey")
+ ## horizontal segments
+ segments(x0=rep(min(x.grid),plotres$Ntip), y0=y.grid,
+ x1=rep(max(x.grid),plotres$Ntip), y1=y.grid, col="grey")
+ }
+
+ ## auxiliary function to plot a single variable
+ ## max size of a symbol is set to SYMBSCALE*cex inches
+ plotaux <- function(x,y,var,symbol,cex){
+ if(any(var[!is.na(var)]<0)) {
+ usebw <- TRUE
+ } else {
+ usebw <- FALSE
+ }
+
+ if(usebw){
+ ispos <- var>0
+ fg.col <- rep("black",length(var))
+ fg.col[ispos] <- "white"
+ bg.col <- rep("white",length(var))
+ bg.col[ispos] <- "black"
+
+ if(symbol == "squares"){
+ symbols(x=x, y=y, squares=abs(var), inches=SYMBSCALE*cex, fg=fg.col, bg=bg.col, add=TRUE)
+ } # end squares
+
+ if(symbol == "circles"){
+ symbols(x=x, y=y, circles=abs(var), inches=SYMBSCALE*cex, fg=fg.col, bg=bg.col, add=TRUE)
+ } # end circles
+
+ } else {
+
+ if(symbol == "squares"){
+ symbols(x=x, y=y, squares=var, inches=SYMBSCALE*cex, fg="white", bg="black", add=TRUE)
+ } # end squares
+
+ if(symbol == "circles"){
+ symbols(x=x, y=y, circles=var, inches=SYMBSCALE*cex, fg="white", bg="black", add=TRUE)
+ } # end circles
+ } # end else
+
+ if(any(is.na(var))){
+ isNA <- is.na(var)
+ points(x[isNA],y[isNA],pch=4,cex=cex.symbol)
+ }
+ } # end plotaux
+
+
+ ## finally plot the data
+ ## carefull : all variables must be plotted in as a single vector, so that
+ ## scaling is the same for all variables
+ ## lapply(alldat, function(X) plotaux(X[,1],X[,2],X[,3],symbol,cex.symbol))
+ plotaux(alldat[,1],alldat[,2],alldat[,3],symbol,cex.symbol)
+
+#### plot labels for variables
+ if(show.var.label) text(x=x.grid, y=rep(min(y.grid)-1.5*y.inset, ncol(dat)), lab=var.label,
+ adj=1, srt=90, cex=cex.label)
+
+#### plot tip labels
+ if(show.tip.label){
+ x.base <- xrange.data[2] + x.inset
+ text(x=rep(x.base,plotres$Ntip), y=1:plotres$Ntip, lab=tip.label, font=font, cex=cex.label, pos=4)
+ }
+
+#### add a legend for symbols
+ if(legend){
+
+ ## Auxiliary function to add the legend
+ ## (x,y): coordinates of the lower-left annotation
+ ## z: a numeric vector whose values are being legended
+ addLegend <- function(x,y,z,cex.legend,cex.label,cex.symbol){
+ z <- z*cex.legend
+ leg.values <- pretty(z,n=4, min.n=1)
+ temp <- length(leg.values)
+ ## make sure to get maximum 4 symbols
+ if(temp>4) {
+ leg.values <- leg.values[c(1,2,temp-1,temp)]
+ }
+
+ leg.txt <- as.character(leg.values)
+
+ ## compute the maximum size taken by symbols in usr coordinates
+ usr.w <- (par("usr")[2]-par("usr")[1]) / ratio.tree # because par("usr") is the one of plot.phylo
+ usr.h <- par("usr")[4]-par("usr")[3]
+ sym.w <- usr.w *
+ ((abs(leg.values)/max(abs(leg.values))) * SYMBSCALE * cex.symbol * cex.legend) / par("pin")[1]
+ sym.h <- usr.h * (SYMBSCALE * cex.symbol * cex.legend) / par("pin")[2]
+
+ ## compute the maximum size taken by annotations in usr coordinates
+ ann.w <- strwidth(leg.txt,units="user",cex=cex.label*cex.legend)
+ ann.h <- strheight(leg.txt,units="user",cex=cex.label*cex.legend)
+
+ ## retain relevant spaces between symbols / annotations
+ space.w.sym <- sapply(1:(length(sym.w)-1),function(i) sum(sym.w[c(i,i+1)]))
+ space.w.ann <- sapply(1:(length(ann.w)-1),function(i) sum(ann.w[c(i,i+1)])) / 2
+ temp <- cbind(space.w.sym, space.w.ann)
+ space.w <- apply(temp,1,max)
+ space.w <- space.w + 0.01*usr.w
+ space.h <- sym.h + ann.h + 0.01*usr.h
+
+ ## define coordinates of annotations and symbols
+ ann.coordX <- c(x, x + cumsum(space.w)) + max(sym.w[1],ann.w[1]) + 0.01*usr.w
+ ann.coordY <- y
+ sym.coordX <- ann.coordX
+ sym.coordY <- y + space.h
+
+ ## plot annotations
+ text(ann.coordX, ann.coordY, leg.txt, cex=cex.label*cex.legend)
+
+ ## plot symbols
+ plotaux(sym.coordX, sym.coordY, leg.values, symbol, cex.symbol*cex.legend)
+ } # end addLegend
+
+ if(!is.null(coord.legend)){
+ x.leg <- coord.legend$x
+ y.leg <- coord.legend$y
+ } else {
+ usr.w <- (par("usr")[2]-par("usr")[1]) / ratio.tree
+ usr.h <- par("usr")[4]-par("usr")[3]
+
+ temp <- lab.height * usr.height / (1 - lab.height) ## need to substract temp from par("usr")[3]
+ y.base <- par("usr")[3] - temp - y.inset ## to get closer the actual par("usr")[3] !
+
+ x.leg <- par("usr")[1] + 0.01 * usr.w
+ y.leg <- y.base ## remember to use y.base instead of par("usr3")[3], which is wrong
+ }
+
+ addLegend(x=x.leg, y=y.leg, z=alldat[,3],
+ cex.legend=cex.legend, cex.label=cex.label, cex.symbol=cex.symbol)
+ ## FIXME ##
+ ## draw a rectangle around the legend
+ #rect.size <- c(diff(range(leg.x)) , diff(c(y.base, max(leg.y))) )
+ #rect(min(leg.x)- rect.size[1]*0.05,
+ # min(y.base) - rect.size[2]*0.05,
+ # max(leg.x) + rect.size[1]*0.05,
+ # max(y.base) + rect.size[2]*0.05)
+ } ## end legend
+
+ return(invisible())
+} # end s.phylo4d
More information about the Adephylo-commits
mailing list