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plot_qual
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plot.qual<-function(x,x.locs=c(0.01,0.99),y.locs=c(0,1),steps=NULL,sp.names=NULL,dt.tx=T,rsc=T, | |
ln.st=NULL,rs.ln=c(3,15),ln.cl='RdYlGn',alpha=0.7,leg=T,rnks=FALSE,...){ | |
require(RColorBrewer) | |
require(scales) | |
if(length(x.locs) != 2 | length(y.locs) != 2) | |
stop('x and y dimensions must be two-element vectors') | |
if(x.locs[1]<0 | x.locs[2]>1 | y.locs[1]<0 | y.locs[2]>1) | |
stop('x and y dimensions must in range of 0--1') | |
dim.x<-c(0,1) #plot dims x | |
dim.y<-c(0,1) #plot dims y | |
wrn.val<-F | |
x[,1]<-as.character(x[,1]) | |
tot.sp<-ncol(x)-1 | |
sp.col<-2:ncol(x) | |
#rescale if T, sort legend for later | |
sp.orig<-x[,sp.col] | |
if(length(rs.ln)==1) rsc<-F | |
if(rsc) x[,sp.col]<-rescale(as.matrix(x[,sp.col]),rs.ln) | |
if(rsc==F & leg) leg<-F #no legend if line widths aren't rescaled | |
#reorder species columns, add rank as integer | |
first.ord<-order(x[1,sp.col],decreasing=T) | |
x[,sp.col]<-x[,sp.col][,first.ord] | |
names(x)[sp.col]<-names(x)[sp.col][first.ord] | |
names(x)[sp.col]<-paste(1:tot.sp,names(x)[sp.col],sep='. ') | |
#list of spp by date, arranged in decreasing order for each date | |
dt.dat.srt<-vector('list',nrow(x)) | |
names(dt.dat.srt)<-x[,1] | |
for(val in 1:nrow(x)){ | |
tmp<-t(x[val,sp.col]) | |
tmp<-tmp[order(tmp,decreasing=T),,drop=F] | |
dt.dat.srt[[val]]<-tmp | |
} | |
#initiate plot object | |
plot(dim.x,dim.y,type='n',axes=F,xlab='',ylab='',...) | |
#subset for steps, if provided | |
if(!is.null(steps)) dt.dat.srt<-dt.dat.srt[names(dt.dat.srt) %in% steps] | |
#plot legend | |
if(leg){ | |
y.locs[1]<-0.05*diff(y.locs)+y.locs[1] | |
leg.txt<-format(round(seq(min(sp.orig),max(sp.orig),length=5),2),nsmall=2,digits=2) | |
leg.wds<-seq(rs.ln[1],rs.ln[2],length=5) | |
legend('bottom',(y.locs[1]-y.olds)/2,col=alpha('black',alpha),lwd=leg.wds,legend=leg.txt,bty='n', | |
horiz=T) | |
} | |
#x locations | |
x.vals<-rep(seq(x.locs[1],x.locs[2],length=length(dt.dat.srt)),each=tot.sp) | |
x.vals<-split(x.vals,x.vals) | |
#y locations, rearranged in loop, exception if dates are plotted | |
if(dt.tx) y.vals<-rev(seq(y.locs[1],y.locs[2],length=tot.sp+1))[-1] | |
else y.vals<-rev(seq(y.locs[1],y.locs[2],length=tot.sp)) | |
#get line colors | |
if(length(ln.cl)==1) | |
if(ln.cl %in% row.names(brewer.pal.info)){ | |
pal.num<-brewer.pal.info[row.names(brewer.pal.info) == ln.cl,1] | |
ln.cl<-brewer.pal(pal.num,ln.cl) | |
} | |
line.cols<-alpha(colorRampPalette(ln.cl)(tot.sp),alpha) | |
#define distance of lines from labels | |
if(is.null(ln.st)){ | |
str.max<-max(strwidth(row.names(dt.dat.srt[[1]]))) | |
if(diff(x.locs)-length(dt.dat.srt)*str.max < 0){ | |
warning('not enough space for lines between columns') | |
wrn.val<-T | |
} | |
else | |
ln.st<-0.2*str.max + str.max/2 | |
} | |
for(val in 1:(length(dt.dat.srt)-1)){ | |
#temp data to plot | |
plt.tmp<-dt.dat.srt[c(val,val+1)] | |
x.tmp<-x.vals[c(val,val+1)] | |
#plot temp text for column, remove spp if rnks | |
rowtxt <- row.names(plt.tmp[[1]]) | |
if(rnks) | |
rowtxt <- gsub('([1-9]*)\\..*', '\\1', rowtxt) | |
text(x.tmp[[1]],y.vals,rowtxt) | |
if(val == length(dt.dat.srt)-1){ | |
rowtxt <- row.names(plt.tmp[[2]]) | |
if(rnks) | |
rowtxt <- gsub('([1-9]*)\\..*', '\\1', rowtxt) | |
text(x.tmp[[2]],y.vals,rowtxt) | |
if(dt.tx){ | |
dt.txt<-substitute(italic(x),list(x=names(plt.tmp)[2])) | |
text(unique(x.tmp[[2]]),y.locs[2],dt.txt) | |
} | |
} | |
if(dt.tx){ | |
dt.txt<-substitute(italic(x),list(x=names(plt.tmp)[1])) | |
text(unique(x.tmp[[1]]),y.locs[2],dt.txt) | |
} | |
srt.ln.y<-match(row.names(plt.tmp[[1]]),row.names(plt.tmp[[2]])) | |
#if no line rescale, use first element of rs.ln | |
if(rsc) lwd.val<-plt.tmp[[1]][,1] | |
else lwd.val<-rep(rs.ln[1],tot.sp) | |
#vector for species selection of line segments | |
if(is.null(sp.names)) sel.sp<-rep(T,tot.sp) | |
else{ | |
sel.names<-unlist(lapply(strsplit(row.names(plt.tmp[[1]]),' '),function(x) x[2])) | |
sel.sp<-(sel.names %in% sp.names) | |
} | |
#for lines | |
if(!wrn.val) | |
segments( | |
x.tmp[[1]][sel.sp]+ln.st, | |
y.vals[sel.sp], | |
x.tmp[[2]][sel.sp]-ln.st, | |
y.vals[srt.ln.y][sel.sp], | |
col=line.cols[sel.sp], | |
lwd=lwd.val[sel.sp] | |
) | |
#resort color vector for next colummn | |
srt.cl.y<-match(row.names(plt.tmp[[2]]),row.names(plt.tmp[[1]])) | |
line.cols<-line.cols[srt.cl.y] | |
} | |
} |
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