I am trying to create a simple dotplot (lattice package) in R with the following data frame:
df<-data.frame(Sediment=c("Algae", "Algae", "Algae", "Bare", "Bare", "Bare", "Dredged", "Dredged", "Dredged"), Rep=c(1,2,3,1,2,3,1,2,3), LeafElongation=c(0, 20.6, 0, 29.1, 41.4, 45.9, 54.1, 22.3, 26.7))
I would like to use marker colors to group the data by Sediment and marker shapes to group data by Rep. This is my code so far:
dotplot(LeafElongation~Sediment, data=df, groups=Sediment, method="jitter", col =
c("darkolivegreen", "darkgoldenrod3", "sienna"), main= "Leaf Elongation: Ramet Plots", ylab="Average total plant leaf elongation (cm)", cex.main=1.7, cex.lab=1.2, cex.axis=1.7)
I have successfully grouped my data by sediment and this is generally how I would like the plot to appear, but I would like to have a different shape for each Rep (circles for 1, diamonds for 2, triangles for 3). I would also like the shapes to be filled rather than open. Additionally, I believe the jitter method is supposed to separate overlapping points so that both can be seen, but it does not appear to be working in this case.
The pch argument is what you are looking for. Just add it to your code and feed it directly with df$Rep. You can remove the argument groups, that now unnecessary.
dotplot(LeafElongation~Sediment, data=df,
method="jitter",
col = c("darkolivegreen", "darkgoldenrod3", "sienna"),
main= "Leaf Elongation: Ramet Plots",
ylab="Average total plant leaf elongation (cm)",
cex.main=1.7, cex.lab=1.2, cex.axis=1.7,
pch = df$Rep)