Sample dataset:
library(ggplot2)
df = read.table(text =
\"id year value1 value2 value3
1 2000 1 2000
Is this what you are looking for?
ggplot(df, aes(y=id)) +
geom_point(aes(x=year, color=value1), size=4) +
geom_point(aes(x=value3, colour ='value3'), size=3) +
geom_point(aes(x=value2, colour ='value2'), size=5) +
scale_colour_manual(name="",
values = c("1"="yellow", "2"="orange", "3"="red",
"value3"="grey", "value2"="black"))

Basically, just putting all possible colour labels in a single list.