> >Dear Yalbi, > >Thank you for using motifStack package and the kind words. > >You can try to use function colorset to get a sample color list like: > >> col <- colorset("AA", "chemistry") >> col > A C D E F G H > I K L M N >"#000000" "#00811B" "#D00001" "#D00001" "#000000" "#00811B" "#2000C7" >"#000000" "#2000C7" "#000000" "#000000" "#800080" > P Q R S T V W > Y >"#000000" "#800080" "#2000C7" "#00811B" "#00811B" "#000000" "#000000" >"#00811B" > > >It is easy to change the colors for each amino acids as you want. And then >use the user defined color set as color of pfm or pcm object. > >Hope this will help you. > > >Yours sincerely, > >Jianhong Ou > >LRB 670A >Program in Gene Function and Expression >364 Plantation Street Worcester, >MA 01605 > > > > >On 10/29/13 7:33 PM, "Yalbi Balderas" <balderas at="" ccg.unam.mx=""> wrote: > >> >>Dear >>Jianhong Ou >> >> >>I write you because I am using your motifStack package to plot several >>amino acid logos, it works fine and it is very helpful, >>however I would like to know if there is an option in which I can choose >>only two colors to represent two different types of amino acids (those >>who binds metal or not), I have tried with several options in colorset >>but none of them is adequate for me. I hope you could tell me what can I >>do. >> >>Thank you very much for your time, >> >> >> >>================================== >>Yalbi Balderas-Mart?nez >>Center for Genomics Sciences >>UNAM >>Mexico >