colors_across_graphs

library(ggplot2)

dat1 <- data.frame(y=c(1,2,3,4,5),
                   x=c("a","b","c","d","f"))

dat2 <- data.frame(y=c(1,2,3,4,5),
                   x=c("b","c","d","e","f"))


plot1 <- ggplot(dat=dat1, 
                aes(x=x, y=y, color=x))+
  geom_point()+
  # this code below here is the same in both graphs
  scale_color_manual(breaks=c("a","b","c","d","e","f"), # so this is all the bacteria groups, across all the graphs
                     values=c("red","orange",
                              "yellow","green",
                              "blue","purple")) # and this is their colors

plot2 <- ggplot(data=dat2,
                aes(x=x, y=y, color=x))+
  geom_point()+
  scale_color_manual(breaks=c("a","b","c","d","e","f"),
                     values=c("red","orange",
                              "yellow","green",
                              "blue","purple"))