Plotting confidence intervals in ggplot

Question

I'd like to do the following plot using ggplot:

GgPlot of Confidence Intervals by Group

Here is an example of the structure of my df (sort of, draw not to scale with the data):

example.df = data.frame(mean = c(0.3,0.8,0.4,0.65,0.28,0.91,0.35,0.61,0.32,0.94,0.1,0.9,0.13,0.85,0.7,1.3), 
                            std.dev = c(0.01,0.03,0.023,0.031,0.01,0.012,0.015,0.021,0.21,0.13,0.023,0.051,0.07,0.012,0.025,0.058),
                            class = c("1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2"),
                            group = c("group1","group2","group1","group2","group1","group2","group1","group2","group1","group2","group1","group2","group1","group2","group1","group2"))

This data frame consists of 16 replicates, each with a given mean and a given standard deviation.

For each replicate I'd like to plot the confidence intervals, where the big dot in my figure example is the mean estimate, and the length of the bar is twice the standard deviation.

Also I'd like to plot two different replicates in the same line but with different coloring, coloring it by class, red is class 1 and blue is class 2.

Finally, I'd like to divide the whole plot into two panels (in the same row) corresponding to the two different groups.

I tried looking into this site, http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/ but couldn't figure out how to automate this for any data frame of this structure, with X number of groups (in this case 2), and K replicates per group (in this case 8, 4 of class 1 and 4 of class 2).

Is there a good way to do this using ggplot or standard r pkg libraries?

You find several examples that may be relevant here. Also, you are much more likely to receive help if you show what you have tried. Questions asking for code must include attempted solutions, why they didn't work, and the expected results — Henrik
@Henrik, my data does not look like that so I had to do lots of processing to get to that data frame, I thought from that data frame structure would be one ggplot line to do the plot but may be wrong. I have tried geom but I haven't been able to put two points two confidence intervals in the same x-axis. — Dnaiel

Didzis Elferts Didzis Elferts · Accepted Answer · 2013-10-26T12:01:14

I suppose that sample data frame you provided isn't build in appropriate way because all values in group1 have class 1, and in group2 all are class 2. So I made new data frame, added also new column named replicate that shows number of replicate (four replicates (with two class values) in each group).

example.df = data.frame(mean = c(0.3,0.8,0.4,0.65,0.28,0.91,0.35,0.61,0.32,0.94,0.1,
                                0.9,0.13,0.85,0.7,1.3), 
                        std.dev = c(0.01,0.03,0.023,0.031,0.01,0.012,0.015,0.021,0.21,
                                  0.13,0.023,0.051,0.07,0.012,0.025,0.058),
                        class = c("1","2","1","2","1","2","1","2","1","2","1",
                                 "2","1","2","1","2"),
                        group = rep(c("group1","group2"),each=8),
                        replicate=rep(rep(1:4,each=2),time=2))

Now you can use geom_pointrange() to get points with confidence intervals and facet_wrap() to make plot for each group.

ggplot(example.df,aes(factor(replicate),
               y=mean,ymin=mean-2*std.dev,ymax=mean+2*std.dev,color=factor(class)))+
  geom_pointrange()+facet_wrap(~group)

enter image description here

Plotting confidence intervals in ggplot

1 Answers