R: ggplot2 barplot and error bar

ggplot2r

Since the new version of ggplot2 (0.9.3), I've problem to plot barplots with errorbars. So I've a dataframe like this :

    group N        val         sd         se         ci
1     206 3 37.2269533  7.9688645  4.6008261 19.7957568
2     207 3  2.0731505  2.2843009  1.3188417  5.6745180
3     208 3  2.2965978  1.4120606  0.8152536  3.5077531
4     209 3  3.1085132  1.1986664  0.6920504  2.9776525
5     210 3  3.3735251  1.9226134  1.1100214  4.7760365
6     211 3  4.0477951  2.9410503  1.6980162  7.3059739
7     212 3  1.2391158  1.2345554  0.7127709  3.0668055
8     213 2  1.3082374  1.1234220  0.7943793 10.0935460

I want to plot for each group the val +- s : I did that before upgrade :

ggplot(dfc, aes(x=factor(group), y=factor(val)) +  geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=val-se, ymax=val+se),width=.1,position=position_dodge(.9))

It gives me that:

Mapping a variable to y and also using stat="bin".
With stat="bin", it will attempt to set the y value to the count of cases in each group.
This can result in unexpected behavior and will not be allowed in a future version of ggplot2.
If you want y to represent counts of cases, use stat="bin" and don't map a variable to y.
If you want y to represent values in the data, use stat="identity".
See ?geom_bar for examples. (Deprecated; last used in version 0.9.2)

So anyone knows how to resolve that ? Thanks

ggplot barplot

Best Answer

Is this what you're after?

my.df <- read.table(text = "group N        val         sd         se         ci
206 3 37.2269533  7.9688645  4.6008261 19.7957568
207 3  2.0731505  2.2843009  1.3188417  5.6745180
208 3  2.2965978  1.4120606  0.8152536  3.5077531
209 3  3.1085132  1.1986664  0.6920504  2.9776525
210 3  3.3735251  1.9226134  1.1100214  4.7760365
211 3  4.0477951  2.9410503  1.6980162  7.3059739
212 3  1.2391158  1.2345554  0.7127709  3.0668055
213 2  1.3082374  1.1234220  0.7943793 10.0935460", header = TRUE)

ggplot(my.df, aes(x = factor(group), y = val)) +  
  geom_bar(position = position_dodge()) + 
  geom_errorbar(aes(ymin=val-se, ymax=val+se))

enter image description here

Any ggplots side-by-side (or n plots on a grid)

The function grid.arrange() in the gridExtra package will combine multiple plots; this is how you put two side by side.

require(gridExtra)
plot1 <- qplot(1)
plot2 <- qplot(1)
grid.arrange(plot1, plot2, ncol=2)

This is useful when the two plots are not based on the same data, for example if you want to plot different variables without using reshape().

This will plot the output as a side effect. To print the side effect to a file, specify a device driver (such as pdf, png, etc), e.g.

pdf("foo.pdf")
grid.arrange(plot1, plot2)
dev.off()

or, use arrangeGrob() in combination with ggsave(),

ggsave("foo.pdf", arrangeGrob(plot1, plot2))

This is the equivalent of making two distinct plots using par(mfrow = c(1,2)). This not only saves time arranging data, it is necessary when you want two dissimilar plots.

Appendix: Using Facets

Facets are helpful for making similar plots for different groups. This is pointed out below in many answers below, but I want to highlight this approach with examples equivalent to the above plots.

mydata <- data.frame(myGroup = c('a', 'b'), myX = c(1,1))

qplot(data = mydata, 
    x = myX, 
    facets = ~myGroup)

ggplot(data = mydata) + 
    geom_bar(aes(myX)) + 
    facet_wrap(~myGroup)

Update

the plot_grid function in the cowplot is worth checking out as an alternative to grid.arrange. See the answer by @claus-wilke below and this vignette for an equivalent approach; but the function allows finer controls on plot location and size, based on this vignette.

Rotating and spacing axis labels in ggplot2

Change the last line to

q + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

By default, the axes are aligned at the center of the text, even when rotated. When you rotate +/- 90 degrees, you usually want it to be aligned at the edge instead:

alt text

The image above is from this blog post.

Best Answer

Related Solutions

R – Side-by-side plots with ggplot2

Any ggplots side-by-side (or n plots on a grid)

Appendix: Using Facets

Update

Rotating and spacing axis labels in ggplot2

Related Topic