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I want to use ggplot to create a line graph, with the values of each 'Molecule' represented by a different line. I want to use 'Family' to colour each line. I am having issues with this and can't seem to represent the individual values as separate lines, nor colour them based on their family.

df.long = melt(df, id.vars = c("Molecule", "Family"), measure.vars = c(3:7)) ggplot(df.long, aes(variable, value)) + geom_line(aes(colour = Molecule)

I end up plotting something like this:

enter image description here

If someone could help me work this out, I would appreciate it.

This is how my data is organized, in wide format:

Molecule Family Pos1 Pos2 Pos3 Pos4 Pos5
A i 2.178 1.289 0.656 0.956 0.711
B ii 1.478 0.889 0.578 0.689 0.444
C ii 1.389 1.078 1.189 0.944 1.844
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1 Answer 1

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To get separate lines for each Molecule you have to map Molecule on the group aes:

library(ggplot2) library(reshape2) df <- read.table(text = "Molecule Family Pos1 Pos2 Pos3 Pos4 Pos5 A i 2.178 1.289 0.656 0.956 0.711 B ii 1.478 0.889 0.578 0.689 0.444 C ii 1.389 1.078 1.189 0.944 1.844", header = TRUE) df.long = melt(df, id.vars = c("Molecule", "Family"), measure.vars = c(3:7)) ggplot(df.long, aes(variable, value)) + geom_line(aes(colour = Family, group = Molecule))

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3 Comments

Holy cow! Thank you so much. What a great fix! Edit: Solved the problem
(: BTW: The reason why we need the group aes is that your x variable is itself a categorical variable. In that case ggplot2 by default uses the variable mapped on x for the grouping, that's why you get the vertical lines.
That makes a lot of sense. So many methods to learn! Much appreciated

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