I know how to create regular plots with error bars for, say, one factor (e.g. experiment) and one measurement (e.g. quality). I first summarize the data to get mean and CI using the summarySE function given on this site. For example:
hrc_id experiment N quality sd se ci
0 FB_IS 77 3.584416 0.6757189 0.07700532 0.15336938
0 FB_ACR 77 3.779221 0.6614055 0.07537416 0.15012064
1 FB_IS 77 3.038961 0.7854191 0.08950681 0.17826826
1 FB_ACR 77 3.129870 0.8483831 0.09668223 0.19255935
...
That way I could plot:
ggplot(d, aes(hrc_id, quality), quality, color = experiment)) +
geom_point(position = position_dodge(width = .5)) +
geom_errorbar(aes(ymin = quality - ci, ymax = quality + ci), width = .5, position = "dodge")

However, now I have to do the same with two measurements—not just quality, but also confidence. For example, my data might look as follows:
hrc_id confidence confidence_ci quality quality_ci
0 3.573718 0.02068321 4.576923 0.02864818
1 3.403846 0.03193104 1.658120 0.04441434
10 3.160256 0.02520483 3.038462 0.04476492
...
How would I go about plotting confidence (with confidence_ci) and quality (with quality_ci) next to each other, for each hrc_id?
I thought I could melt the dataframe so that confidence and quality would be the measurement variables, but then I lose the CI values that belong to them.