http://novita-med.pl/?komarivske=jezuici-lodz-msza-dla-singli&100=d3 Customize the color, order and label of the legend in ggplot2
Use scale_colour_manual()

fougères rencontre hetero scale_colour_manual(values = c("red", "blue"), breaks = c("S2", "S1"), labels = c("sample1", "sample2"))

http://had.co.nz/ggplot2/scale_manual.html