[R] keep track of selected observations over time

Wed Jan 24 18:26:17 CET 2007

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

  Here is my problem again:

  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 at 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 at 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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