From: Petr Pikal <petr.pikal_at_precheza.cz>

Date: Thu 25 Jan 2007 - 14:24:27 GMT

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri Jan 26 01:36:57 2007

Date: Thu 25 Jan 2007 - 14:24:27 GMT

Hi

On 24 Jan 2007 at 18:26, Jenny persson wrote:

Date sent: Wed, 24 Jan 2007 18:26:17 +0100 (CET) From: Jenny persson <jenny197806@yahoo.se> To: r-help@stat.math.ethz.ch Subject: Re: [R] keep track of selected observations over time

*>
*

> Thanks Peter, I forgot that the mailinglist only accept the pdf and

*> ps. file.
**>
*

Well, not sure if I understand what you want (your example is not reproducible), but a boxplot beside of making actual plot also returns invisibly a structure for plotting, actually a list. So you can call

b.str<- boxplot(.....)

and if you go through b.str you can find

$out and $group values, which indicate outliers. Then you can do e.g.

sel <- your.data[,2] %in% b.str$out[ddd$group == 1]

to get logical vector which points are marked as outliers in your first column.Then

your.data[sel,]

gives you appropriate rows which you can use e.g. for adding lines

lines(1:4, your.data[sel,][1,-1])

**HTH
**

Petr

> 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@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
**>
**>
**> ---------------------------------
**>
**>
**>
**> ______________________________________________
**> R-help@stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide
**> http://www.R-project.org/posting-guide.html and provide commented,
**> minimal, self-contained, reproducible code.
**>
**>
**>
**>
**>
**>
**>
**> ---------------------------------
**>
**>
*

Petr Pikal

petr.pikal@precheza.cz

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri Jan 26 01:36:57 2007

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