R ggplot2: boxplots with wilcoxon significance levels, and facets. Show only significant comparisons with asterisks

Question

Following up on this question and for the sake of completeness, I modified the accepted answer and customized the resulting plot, but I am still facing some important proble

Answer 1

Constructing ggplots in a loop has always been known to produce confusing results, and for the explanation of point 1 I'll refer to this question and many others. There's also a hint there about evaluating the ggplot object on the spot, e.g. via print. Re point 2, you were close, a bit of debugging with trial and error helped. Here's the complete code for plot.list:

plot.list=function(mydf, pv.final, addkw, a, myPal){
    mylist <- list()
    i <- 0
    for (sp in unique(mydf$Species)){
        i <- i+1
        mydf0 <- subset(mydf, Species==sp)
        addkw0 <- subset(addkw, Species==sp)
        pv.final0 <- pv.final[grep(sp, pv.final$group1), ]
        num.signif <- sum(pv.final0$p.value <= 0.05)
        P <- ggplot(mydf0,aes(x=both, y=value)) +
            geom_boxplot(aes(fill=Species)) +
            stat_summary(fun.y=mean, geom="point", shape=5, size=4) +
            facet_grid(~Species, scales="free", space="free_x") +
            scale_fill_manual(values=myPal[i]) +
            geom_text(data=addkw0, hjust=0, size=4.5, aes(x=0, y=round(max(mydf0$value, na.rm=TRUE)+0.5), label=paste0("KW p=",p.value))) +
            geom_signif(test="wilcox.test", comparisons = a[which(pv.final0$p.value<=0.05)],#I can use "a"here
                        map_signif_level = F,            
                        vjust=0,
                        textsize=4,
                        size=0.5,
                        step_increase = 0.05)
        if (i==1){
            P <- P + theme(legend.position="none",
                           axis.text.x=element_text(size=20, angle=90, hjust=1),
                           axis.text.y=element_text(size=20),
                           axis.title=element_blank(),
                           strip.text.x=element_text(size=20,face="bold"),
                           strip.text.y=element_text(size=20,face="bold"))
        } else{
            P <- P + theme(legend.position="none",
                           axis.text.x=element_text(size=20, angle=90, hjust=1),
                           axis.text.y=element_blank(),
                           axis.ticks.y=element_blank(),
                           axis.title=element_blank(),
                           strip.text.x=element_text(size=20,face="bold"),
                           strip.text.y=element_text(size=20,face="bold"))
        }
        P2 <- ggplot_build(P)
        P2$data[[4]]$annotation <- rep(subset(pv.final0, p.value<=0.05)$map.signif, each=3)
        P <- ggplot_gtable(P2)
        mylist[[sp]] <- list(num.signif, P)
    }
    return(mylist)
}

Note that we can no longer modify the plot via ggplot semantics, since we already applied ggplot_build/ggplot_gtable, so scale modification is no longer possible. If you want to preserve it, move it inside the plot.list function. So, changing to

grid.arrange(grobs=lapply(p.list, function(x) x[[2]]), 
             ncol=length(unique(mydf$Species)), top="Random title", left="Value")

yields

That's not a complete solution, of course, but I hope that helps.