R/rateLegend.R

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

############################################
#	Internal function called by plot.bammdata(...)
#
#
rateLegend = function(colobj, log = FALSE) {
	opar = par(no.readonly = TRUE);
    cat("Click once where you want the lower left corner of the figure\n");
    cxy = locator(n = 1);
    xc = (grconvertX(cxy$x, to = "ndc"));
    yc = (grconvertY(cxy$y, to = "ndc"));
    ofs = min(1 - xc, 1 - yc);
    fig = c(xc, xc + ofs, yc, yc + ofs);
    par(fig = fig, new = TRUE, xpd = TRUE, mar = c(1.5, 1.5, 0.25, 0.25));
    plot.new();
    x = colobj[,1];
    y = colobj[,2];
   	plot.window(xlim = c(min(0,min(x)), max(x)), ylim = c(0, max(y)));
   	segments(x, y, x, 0, lend = 2, col = colobj[,3]);
   	axis(1, signif(seq(min(0,min(x)), max(x), length.out = 5), 2), xaxs = "i", cex.axis = 0.75, tcl = NA, mgp = c(0, 0.25, 0));
   	axis(2, round(seq(0, max(y), length.out = 3), 0), las = 1, yaxs = "i", cex.axis = 0.75, tcl = NA, mgp = c(0, 0.25, 0));
    if (log == FALSE) mtext("Evolutionary Rate", 1, line = 1, cex = 0.75)
    else mtext("Evolutionary Rate (log)", 1, line = 1, cex = 0.75);
    mtext("Density", 2, line = 1, cex = 0.75);
    par(opar);
}

# histRates = function(rates,pal,NCOLORS) {
	# opar = par(no.readonly = TRUE);
	# fx = density(rates);
	# dpal = c('BrBG','PiYG','PuOr','RdBu','RdGy','RdYlBu','RdYlGn','Spectral');
	# if(length(pal) == 3) {
		# rate.colors = colorRampPalette(pal,space='Lab')(NCOLORS);	
	# }
	# else if(pal %in% dpal) {
		# rate.colors = colorRampPalette(rev(brewer.pal(3,pal)),space='Lab')(NCOLORS);
	# }
	# else if(pal == 'temperature') {
		# rate.colors = gplots::rich.colors(NCOLORS);	
	# }
	# qx = quantile(rates,seq(0,1,length.out = NCOLORS+1));
	# cat("Click once where you want the lower left corner of the figure\n");
	# cxy = locator(n=1);
	# xc = (grconvertX(cxy$x,to='ndc'));
	# yc = (grconvertY(cxy$y,to='ndc'));
	# ofs = min(1 - xc, 1 - yc);
	# fig = c(xc,xc+ofs,yc,yc+ofs);
	# par(fig = fig, new=TRUE, xpd=TRUE, mar=c(1.5,1.5,0.25,0.25));
	# plot.new();
	# plot.window(xlim=c(min(0,min(fx$x)),max(fx$x)),ylim=c(0,max(fx$y)));
	# for(i in 1:length(fx$x)) {
		# index = which(qx > fx$x[i])[1];
		# if(is.na(index)) break;
		# if(index > 1) index = index - 1;
		# bcol = rate.colors[index];
		# segments(fx$x[i],fx$y[i],fx$x[i],0,lend=2,col=bcol);
	# }
	# axis(1,signif(seq(min(0,min(fx$x)),max(fx$x),length.out=5),2),pos=0,cex.axis=0.75,tcl=NA,mgp=c(0,0.25,0));
	# axis(2,round(seq(0,max(fx$y),length.out=3),0),las=1,pos=0,cex.axis=0.75,tcl=NA,mgp=c(0,0.25,0));
	# mtext('Evolutionary Rate',1,line=1,cex=0.75);
	# mtext('Density',2,line=1,cex=0.75);
	# par(opar);
# }