I have a table similar to the following which shows the number of samples which tested positive for viruses within different species:
Species Virus NoTested NoPositive Prevalence LowerCI UpperCI
1 1 100 46 0.46 0.4 0.5
2 1 80 23 0.29 0.2 0.3
3 1 96 3 0.03 0 0.1
1 2 133 45 0.34 0.2 0.5
2 2 23 10 0.43 0.3 0.5
3 2 75 16 0.21 0.1 0.3
1 3 88 24 0.27 0.2 0.3
2 3 94 12 0.13 0.1 0.2
3 3 65 34 0.52 0.4 0.6
I want to create a grouped bar graph such that I can show the proportion of positive samples for each species, in sets according to virus. I also want to add error bars showing confidence intervals.
I have tried doing this in ggplot using geom_bar(), but it gives me a really ugly stacked plot.
bar1<-ggplot(sppPrev3, aes(Species, Prevalence, colour=Virus))
see: this link a lot of info about graphing.
also, maybe try using barplot(t(dataframe), beside = TRUE)
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