Question

Can I make such a plot with ggplot2?

# data
require(vegan)
data(dune)
data(dune.env)

# RDA
RDA <- rda(dune ~ A1, data = dune.env)

# extract species scores
df <- data.frame(spec_scores = scores(RDA)$species[ , 1], 
                 taxa = rownames(scores(RDA)$species))
df <- df[abs(df$spec_scores) > 0.05, ]

# plot
par(mar = c(5,4,4,8))
# boxplot of sites-scores along A1-axis
boxplot(scores(RDA)$sites[ , 1] ~ dune.env$Management)
abline(h = 0, lty = "dotted")

# add species scores to plot
rug(df$spec_scores, side=4)
linestack(df$spec_scores, labels=df$taxa, at = par("usr")[2], add = TRUE, hoff = 1)

Basicly I am looking for a way how to plot a labelled rug beneath the boxplot.

Any hints or suggestions?

Answer 1

This is solution only using ggplot2, so it won’t be most elegant one.

I started with first steps as suggested by @Eric Fail.

require(vegan)
data(dune)
data(dune.env)

# RDA
RDA <- rda(dune ~ A1, data = dune.env)

# extract species scores
df1 <- data.frame(RDA.scores = scores(RDA)$sites[ , 1], Management = dune.env$Management)
df2 <- data.frame(y = scores(RDA)$species[ , 1], taxa = rownames(scores(RDA)$species))
# Order data according to species scores
df2<-df2[order(df2$y),]

# define values for rugs (segments). 4.9 and 5.0 used because data has 4 levels (+1)
df2$x=4.9
df2$xend=5

# define coordinates for names (30 is number of species)
df2$yend2<-seq(min(df1$RDA.scores),max(df1$RDA.scores),length.out=30)
df2$xend2=5.3

# plot
P <- ggplot(data = df1, aes( x = Management, y = RDA.scores) ) + 
     geom_segment(y=0,yend=0,x=0,xend=5, lty=2, size = I(0.3)) + 
     geom_boxplot() + 
     #add extra levels to get space
     scale_x_discrete(limits=c("BF", "HF", "NM", "SF", "","")) + 
     #set y scale
     scale_y_continuous(limits=c(-3,5),expand=c(0,0)) +
     #add rugs as segments and add segments connecting rugs and texts
     geom_segment(data= df2, mapping=aes(x=x,xend=xend,y=y,yend=y), size = I(0.3)) +
     geom_segment(data= df2, mapping=aes(x=xend,xend=xend2,y=y,yend=yend2), size = I(0.4)) +
     #add texts
     geom_text(data=df2,mapping=aes(x=xend2+0.1,y=yend2,label=taxa),hjust=0, size=3) +
     #add rectangular to imitate box around plot
     geom_rect(xmax=5,xmin=0.4,ymax=5,ymin=-3,colour="black",fill=NA)

# Final adjustments of plot
P+theme(axis.line=element_blank(),
        panel.grid=element_blank(),
        panel.background=element_blank())