side by side barcharts

bar_charts_alt.R

# http://timotheepoisot.fr/2013/02/17/stacked-barcharts/
 
library(RColorBrewer)
 
Abund = round(matrix(runif(200,0,1),nc=10),2)
Abund = Abund/max(Abund)
 
rownames(Abund) = LETTERS[c(1:nrow(Abund))]
colnames(Abund) = letters[c(1:ncol(Abund))]
 
# This will give us a site/abundance matrix. The next step is to create a plot with nothing in it:
 
par(las=2)
X = c(1:nrow(Abund))
Y = c(1:ncol(Abund))
 
pal = colorRampPalette(brewer.pal(9,'Paired'))(nrow(Abund))
image(X,Y,Abund,col='white',axes=FALSE,bty='n')
 
# It's easy to make it so that the width of each sub-plot is proportional to the relative abundance of each species.Then, for each row/line (and I'm aware this is not optimized at all), we will draw a vertical bar. Each taxon (i.e. each column in our graph) will have its own sub-plot. The size can be fixed, or equal. But this allows comparison of species abundances across dates.
 
for(ro in 1:nrow(Abund)){
    for(co in 1:ncol(Abund)){
        rect(ro-0.5, co-0.4, ro-0.5+Abund[ro,co]*0.9, co+0.4,border=NA,col=pal[ro])
    }}
 
# Finally, let's add reference lines for each species, and the site/species names on axes:
abline(v=X-0.5,col='darkgrey',lwd=2)
axis(2,at=c(1:ncol(Abund)),labels=colnames(Abund),col=NA)
axis(1,at=c(1:nrow(Abund)),labels=rownames(Abund),col=NA)