Question

I am quite new to ggplot2, so forgive me if this post is too stupid.
I used the following code to plot the data, but I am not able to get the style that I need for publication.

In the output, I need:

1. a legend. In my data case, there is nothing after opts(legend.position="top") I have no idea why. And I also would like to split the legend into 3 columns like columns=3 in auto.key of lattice

2. Colorize the bars using grey system (eg, fill=c("white","grey20","grey70"))according to factor pl, but it seems that I cannot change the style with scale_colour_manual

3. turn around the labels on the x-axis into horizontal.

4. maybe a y-axis? But,do you think it is necessary?

BTW, I have no idea how to prepare a figure for publication, so, any suggestion is very welcome!

library(ggplot2)
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")) 

Answer 1

Here are some pointers:

1. To get a horizontal legend, use opts(legend.direction="horizontal")

2. To change the fill of the bars, you have to specify scale_fill_manual(values=c("white", "grey20", "grey70")). In your example, you have correctly mapped fill to pl. The only missing step is to map the manual scale to fill, rather than colour. Colour generally refers to the outline of the bar, and fill refers to the inside of the bar.

3. To rotate the angle of axis text, use opts(axis.text.x = theme_text(angle=45)). The default orientation is horizontal, so I use 45 degrees for illustration.

4. I don’t know what you mean by “maybe a y-axis”. Perhaps you don’t want to display the y-axis, in which case you can suppress it by opts(axis.title.y = theme_blank())

Note that your example was not reproducible, so I had to invent some data. You can make it easier for us to respond if you ensure your example is reproducible:

• There is no data for year
• There is a reference to trt in your data.frame
• You set up data for grp but then refer to it as gp

My code:

dat.df <- data.frame(
    gp = gl(3, 36, 108, labels=c("A", "B", "C")),
    yr = sample(2000:2010, 108, replace=TRUE),
    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.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")+#, position="dodge"
    facet_grid(variable~facet, scale="free_y")+
    scale_fill_manual(values=c("white", "grey20", "grey70")) +
    opts(
        legend.position="top", 
        legend.direction="horizontal",
        axis.text.x = theme_text(angle=45),
        axis.title.y = theme_blank()
    )