From: Jenny persson <jenny197806_at_yahoo.se>

Date: Wed 24 Jan 2007 - 17:26:17 GMT

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Received on Thu Jan 25 18:34:33 2007

Date: Wed 24 Jan 2007 - 17:26:17 GMT

Thanks Peter, I forgot that the mailinglist only accept the pdf and ps. file.

Attached is a graph of four boxplots from one patient’s data at four time points, i.e. each boxplot presents the data at each time point. At day 0 there are 5 extreme values from five peptide sequences (please see the below data). Since the response is changing over time, some of these five extreme values at day 0 may be lower or higher at day 56, 112 and 252. How can I trace the location of each peptide sequence that has extreme value at day 0 on the box plots at day 56, 112 and 252 by color or number coding. For example, the most five responding peptides can be ranked from 5 (highest value) to 1 (lowest), so if I do the graph again I would see the five extreme values at day 0 as numbers 5-1 and each of these numbers can be any where on the box plot at day 56, 112 and 252 or instead of the rank numbers using the peptide sequence that corresponds to each value. Alternatively, the locations of each peptide sequence at the four time points could be linked by a line. I would like to repeat this procedure for time point 56, 112 and 252 as well. That is, at day 56, I want trace where on the box plot at day 0, 112 and 252, each of the four peptide sequences that have highest responses is. Again, these four values/peptides can be presented by different colors, numbers or their peptide sequences that distinguish them from the other most responding peptides at day 0, 112 and 252. Can I do the four procedures at the same time, I mean, if at each time point I want to keep track of where the most peptide responses from this time point are, then the total number of peptides at the four time points could be 20. That is for each box plot, there will be 20 id numbers corresponding to each peptide at respectively time point. The graph can be kind of messy.

I have a simple solution of how to see the most responding peptides changing over time, by plotting each peptide’s responses at the four time points. But I haven’t managed the procedure above. If you have any suggestion how I can do this in R, I would be very thankful.

Many thanks

Jenny

Part of the data:

> pat1[1:20,]

peptides P1_D0 P1_D56 P1_D112 P1_D252

1 AAAKKGSEQTLKS -0.06181601 -0.12610877 -0.057898384 -0.02126862 2 AAAAPASEDEDDE -0.10972387 -0.17174722 -0.136468783 -0.16262501 3 AAAAVSSAKRSLR 0.64156129 1.02630879 0.079891841 0.29757984 4 AAAKKGSEQESVK -0.54943062 -0.34311337 -0.338910367 -0.14526498 5 AAANLTKIVAYLG -1.72207627 -1.63326368 -0.459839317 -0.63302448 6 AACGRISYNDMFE 0.52513671 0.65123495 1.151866644 1.49481479 7 AAEAEKAASESLR -0.69366543 -0.47038765 -0.144156174 -0.16042556 8 AAEHAQSCRSSAA -0.13373130 -0.09229543 -0.102485597 -0.09782440 9 AAERHARLNDSYRLQ -0.19316423 -0.33164239 -0.033764989 -0.11734969 10 AAETISAARALPS -0.49632307 -0.53666696 -0.263024663 -0.18231712 11 AAEVQRFNRDVDETI -0.80014439 -0.91002202 -0.257201702 -0.12391146 12 AAEWTANVTAEFK -0.41544438 -0.10980658 -0.288133150 -0.32022460 13 AAGIQWSEEETED -0.04015673 0.08529726 0.002471231 0.07599156 14 AAGPALSPVPPVV -0.26795462 -0.36739148 -0.512049278 -0.25449224 15 AAGPPPSEGEEST -1.59272674 -1.69729759 -0.843351943 -0.49271773 16 AAKIASRQPDSHI -0.40722382 -0.27236225 -0.224539441 -0.32998813 17 AAKIQASFRGHMA 2.41234976 2.84435484 0.160852331 0.80197802 18 AALDLGGSSDPYV -1.21202038 -1.25109705 -0.259515922 -0.24351352 19 AALEPGPSESLTA -2.00256570 -1.57566020 -0.390584034 -0.23682626 20 AALLELWELRRQQYE 1.42797600 1.33539104 1.486154861 1.67471189 par(las=1) # all axis labels horizontal boxplot(data.frame(pat1[,c(2:5)]), pars = list(boxwex = 0.4, staplewex = 0.8, outwex = .5), boxfill="lightblue",border=c(3:6), names=c("Day 0", "56 days","112 days", "252 days"), col.main="blue", main ="Averaged peptide response at 4 different time points for patient 200001",cex.main=0.9, font.main=0.9)

Peter Konings <peter.l.e.konings@gmail.com> skrev: Dear Jenny,

Your post did not have an attachment. The mailing list software strips most attachments away: see the 'technical details of posting' section of the posting guide at: http://www.r-project.org/posting-guide.html.

**HTH
**

Peter.

On 1/24/07, Jenny persson < jenny197806@yahoo.se > wrote: Dear all,

Attached is a description of my data, graph and the problem which I need help with. Hope you have time to open the file and help me out.

Many thanks,

Jenny

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