How to label the barplot in ggplot with the labels in another test result?

I would like to label my plot with the label output of a test, eg., LSD test output (a, b, ab, etc) using LSD.test in library agricolae. Here is the running example.

library(ggplot2) 
library(agricolae)
wt<-gl(3,4,108,labels=c("W30","W60","W90")) 
pl<-gl(3,12,108,labels=c("P0","P1","P2")) 
gp<-gl(3,36,108,labels=c("A","B","C")) 

dat<-cbind(
  A=runif(108),
  B=runif(108,min=1,max=10),
  C=runif(108,min=100,max=200),
  D=runif(108,min=1000,max=1500)
) 
dat.df<-data.frame(wt,pl,gp,dat) 
dat.m<-melt(dat.df) 

ggplot(dat.m,aes(x=wt,y=value,group=pl,facet=gp,fill=pl))+         
  stat_summary(fun.y=mean,geom="bar",size=2,position="dodge")+         
  stat_summary(fun.ymin=function(x)(mean(x)-sd(x)/sqrt(length(x))),geom="errorbar", 
  fun.ymax=function(x)(mean(x)+sd(x)/sqrt(length(x))),position="dodge")+
  facet_grid(variable~facet,scale="free_y")+ 
  opts(legend.position="top")+                      
  scale_colour_manual(values = c("red", "blue", "green"))

Normally, in other library, I tested the data, and pass the label to the text plot, but is it possible to do it in ggplot? eg., in stat_summary(), that use the LSD.test within fu开发者_开发知识库n.y?

To achieve this, you have to create another label layer using geom_text and specify its own dataset.

Expanding on the example in lsd.test in package agricolae:

library(agricolae)
library(ggplot2)

data(sweetpotato)
model <- aov(yield~virus, data=sweetpotato)
lsd <- LSD.test(model,"virus",p.adj="bon")

ggplot() + 
  stat_summary(data=sweetpotato, aes(x=virus, y=yield), fun.y=mean, geom="bar") +
  geom_text(data=lsd, aes(x=trt, y=means, label=round(means, 1)), vjust=0)

you can try this

first, defined a vector based on the pvalue, like this:

padj=ifelse(pval<0.001,'*','')

then, add padj column to your data.fram,

 head(df)
                                name               type number padj
1                  metabolic process biological_process    968    *
2                 catalytic activity molecular_function    801    *
3         cellular metabolic process biological_process    617    *
4               biosynthetic process biological_process    357    *
5 cellular protein metabolic process biological_process    279     
6                          cytoplasm cellular_component    202    *

and finally, add geom_text to your plot

p <- ggplot(data=df, aes(x=name,y=number,fill=type))+
geom_bar(position=position_dodge())+
scale_fill_brewer(palette="Set2")+
geom_text(aes(label=padj), vjust=0.25,hjust=0.25)
p