Barplot with significant differences and interactions?

Question

I would like to visualize my data and ANOVA statistics. It is common to do this using a barplot with added lines indicating significant differences and interactions. How do you make plot like this using R? This is what I would like: Significant differences: Significant interactions: Background I am currently using `barplot2{ggplots}` to plot bars and confidence intervals, but I am willing to use any package/procedure to get the job done. To get the statistics I am currently using `TukeyHSD{stats}` or `pairwise.t.test{stats}` for differences and one of the anova functions (`aov`, `ezANOVA{ez}`, `gls{nlme}`) for interactions. Just to give you an idea, this is my current plot:

Accepted Answer

As you are using function `barplot2()` from library `gplots`, will give example using this approach.

First, made barplot as given in help file of `barplot2()` function. `ci.l` and `ci.u` are fake confidence interval values. Barplot should be saved as object.

```
hh <- t(VADeaths)[1:2, 5:1]
mybarcol <- "gray20"
ci.l <- hh * 0.85
ci.u <- hh * 1.15
mp <- barplot2(hh, beside = TRUE,
               col = c("grey12", "grey82"),
               legend = colnames(VADeaths)[1:2], ylim = c(0, 100),
               cex.names = 1.5, plot.ci = TRUE, ci.l = ci.l, ci.u = ci.u)
```

If you look on object `mp`, it contains x coordinates for all bars.

```
 mp
     [,1] [,2] [,3] [,4] [,5]
[1,]  1.5  4.5  7.5 10.5 13.5
[2,]  2.5  5.5  8.5 11.5 14.5
```

Now I use upper confidence interval values to calculate coordinates for y values of segments. Segments will start at position that is 1 higher then the end of confidence intervals. `y.cord` contains four rows - first and second row correspond to first bar and other two rows to second bar. Highest y value is calculated from the maximal values of confidence intervals for each bar pair. `x.cord` values just repeat the same values which are in `mp` object, each 2 times.

```
y.cord<-rbind(c(ci.u[1,]+1),c(apply(ci.u,2,max)+5),
          c(apply(ci.u,2,max)+5),c(ci.u[2,]+1))
x.cord<-apply(mp,2,function(x) rep(x,each=2))
```

After barplot is made use `sapply()` to make five line segments (because this time there are 5 groups) using calculated coordinates.

```
sapply(1:5,function(x) lines(x.cord[,x],y.cord[,x]))
```

To plot texts above the segments calculate x and y coordinates, where x is middle point of two bar x values and y value is calculated from the maximal values of confidence intervals for each bar pair plus some constant. Then use function `text()` to add information.

```
x.text<-colMeans(mp)
y.text<-apply(ci.u,2,max)+7
text(c("*","**","***","NS","***"),x=x.text,y=y.text)
```

Barplot with significant differences and interactions?

Solution

Problem

Related problems