From: Umesh Rosyara <rosyaraur_at_gmail.com>

Date: Fri, 11 Mar 2011 07:01:15 -0500

Date: Fri, 11 Mar 2011 07:01:15 -0500

Thank you for helping me and this solved the problem....

Best Regards

Umesh R

From: foolish.android_at_gmail.com [mailto:foolish.android_at_gmail.com] On Behalf
Of Felix Andrews

Sent: Friday, March 11, 2011 4:05 AM

To: Umesh Rosyara

Cc: R mailing list; Deepayan.Sarkar_at_r-project.org
Subject: Re: [R] still a problem remainingRE: Data lebals xylattice plot:
RE: displaying label meeting condition (i.e. significant, i..e p value less
than 005) in plot function

Yes, it is intersect rather than intersection, sorry.

And in panel.text() the x and y were switched, so just reverse the first two arguments.

Thats what comes from posting from an iGizmo with no R to test my code.

2011/3/11 Umesh Rosyara <rosyaraur_at_gmail.com>:

> Thank you so much for the advice. The R could not find function

*> "intersection". Do I need additional package to have this function active.
*

I

> tried "intersect" instead has no effect.

*>
**> xyplot(p ~ xvar|chr, data=dataf,
**> panel=function(x, y, subscripts){
**> panel.xyplot(x, y)
**> ok= intersection(subscripts, which(dataf$p < 0.05))
**> with(dataf[ok,], panel.text(p, xvar, name))
**> }, as.table=T, subscripts=T)
**>
**>
**> Best Regards
**>
**> Umesh R
**>
**>
**>
**>
**> ________________________________
**> From: foolish.android_at_gmail.com [mailto:foolish.android_at_gmail.com] On
*

Behalf

*> Of Felix Andrews
*

> Sent: Thursday, March 10, 2011 7:01 AM

*> To: Umesh Rosyara
**> Cc: R mailing list; Deepayan.Sarkar_at_r-project.org
**> Subject: Re: [R] still a problem remainingRE: Data lebals xylattice plot:
**> RE: displaying label meeting condition (i.e. significant, i..e p value
*

less

*> than 005) in plot function
**>
*

> Notice that pvals is a subset of dataf so 'subscripts' can not be

*> applied directly to pvals. Instead you should do the subsetting inside
**> the panel function. e.g.
**> ok <- intersection(subscripts, which(dataf$p < 0.05))
**> with(dataf[ok,], panel.text(p, xval, name))
**>
**>
**> By the way you should include the dots (...) in your panel function
**> arguments and pass them on to panel.xyplot.
**>
**>
**> On Thursday, 10 March 2011, Umesh Rosyara <rosyaraur_at_gmail.com> wrote:
**>> Lattice-experts:
**>> Thank you for those who have responded earlier. I have not got a perfect
**>> solution yet but tried several ways, unless anybody really lattice killer
**>> steps up, I will leave it and see alternatives. Sorry to send it again.
**>>
**>>
**>>
**>> #Data
**>>
**>> name <- c(paste ("M", 1:1000, sep = ""))
**>> xvar <- seq(1, 10000, 10)
**>> chr <- c(rep(1,200),rep(2,200), rep(3,200), rep(4,200), rep(5,200))
**>> set.seed(134)
**>> p <- rnorm(1000, 0.15,0.05)
**>> dataf <- data.frame(name,xvar, chr, p)
**>> dataf$chr <- as.factor(dataf$chr)
**>>
**>>
**>>
**>> #subset data
**>>
**>> pvals <- dataf[dataf$p < 0.05,]
**>>
**>>
**>>
**>> # unsuccessful commands
**>>
**>> xyplot(p ~ xvar|chr, data=dataf,
**>> panel=function(x, y, subscripts){
**>>
**>> panel.xyplot(x, y)
**>>
**>> panel.xyplot(pvals$xvar[subscripts],pvals$p[subscripts], pch=6)
**>> panel.abline(h=0.01, col="red")
**>>
**>>
**>> panel.text(pvals$xvar[subscripts], pvals$p[subscripts],
**>> pvals$name[subscripts], col="green2")
**>>
**>>
**>> }, as.table=T, subscripts=T)
**>>
**>>
**>>
**>>
**>>
**>> Best Regards
**>>
**>> Umesh R
**>>
**>>
**>>
**>>
**>> _____
**>>
**>> From: Bert Gunter [mailto:gunter.berton_at_gene.com]
**>> Sent: Tuesday, March 08, 2011 12:00 AM
**>> To: Umesh Rosyara
**>> Cc: Jorge Ivan Velez; Dennis Murphy; sarah.goslee_at_gmail.com; R mailing
**>> list
**>> Subject: Re: still a problem remainingRE: [R] Data lebals xylattice plot:
**>> RE: displaying label meeting condition (i.e. significant, i..e p value
**>> less
**>> than 005) in plot function
**>>
**>>
**>>
**>> As I believe I already told you in my original reply, you have to make
**>> use of the subscripts argument in the panel function to subscript the
**>> P values etc. vector to be plotted in each panel. Something like:
**>> (untested)
**>>
**>> panel = function(x, y,subscripts,...) {
**>> panel.xyplot(x, y,...)
**>> panel.abline(h=0.01, col="red")
**>> panel.text(xv1[subscripts], p1[subscripts],
**>> n1[subscripts], col="green2")
**>> }
**>>
**>>
**>> Also,in future, please send plain text email, as requested in the
**>> guide. Your message was in an annoying blue font in my gmail reader.
**>>
**>> Cheers,
**>> Bert
**>>
**>>
**>> On Mon, Mar 7, 2011 at 5:26 PM, Umesh Rosyara <rosyaraur_at_gmail.com>
*

wrote:

>>> Hi Lattice Users

*>>>
**>>> I have been working to fix this problem, still I am not able to solve
**>> fully.
**>>> I could label those names that have pvalue less than 0.01 but still the
**>>> label appears in all compoent plots eventhough those who do have the
**>> pvalue
**>>> ! How can I implement it successuflly to grouped data like mine. You
*

help

*>> is
*

>>> highly appreciated.

*>>>
**>>> #my data
**>>> name <- c(paste ("M", 1:1000, sep = ""))
**>>> xvar <- seq(1, 10000, 10)
**>>> chr <- c(rep(1,200),rep(2,200), rep(3,200), rep(4,200), rep(5,200))
**>>> set.seed(134)
**>>> p <- rnorm(1000, 0.15,0.05)
**>>> dataf <- data.frame(name,xvar, chr, p)
**>>> dataf$chr <- as.factor(dataf$chr)
**>>>
**>>> # lattice plot: As far as I can go now ! little progress but final push
**>>> required !
**>>> require(lattice)
**>>> pvals <- dataf[dataf$p < 0.01,]
**>>> p1 <- pvals$p
**>>> n1 <- pvals$name
**>>> xv1 <- pvals$xvar
**>>> xyplot(p ~ xvar|chr, data=dataf,
**>>> panel = function(x, y) {
**>>> panel.xyplot(x, y)
**>>> panel.abline(h=0.01, col="red")
**>>> panel.text(xv1, p1, n1, col="green2")
**>>> })
**>>>
**>>> Thank you in advance.
**>>>
**>>> Best Regards
**>>>
**>>> Umesh R
**>>>
**>>>
**>>>
**>>> ________________________________
**>>> From: Bert Gunter [mailto:gunter.berton_at_gene.com]
**>>> Sent: Sunday, March 06, 2011 10:50 AM
**>>> To: Umesh Rosyara
**>>> Cc: Jorge Ivan Velez; Dennis Murphy; sarah.goslee_at_gmail.com; R mailing
**>> list
**>>> Subject: Re: [R] Data lebals xylattice plot: RE: displaying label
*

meeting

*>>> condition (i.e. significant, i..e p value less than 005) in plot
*

function

*>>>
*

>>> This is easy to do by specifying xyplot's panel function. Assuming

*>>> only one panel -- otherwise you need to pass the subscripts arguments
**>>> to choose the values belonging to the panel -- somethings like:
**>>>
**>>> xyplot(y~x, pvals = pvals,..., ## pvals is your vector of small p
**>>> values with e.g. NA's elsewhere
**>>> panel = function(x,y, pvals,...) {
**>>> panel.xyplot(...)
**>>> panel.text((x,y, pvals,...)
**>>> } )
**>>>
**>>> This is obviously just a sketch and will not work as written. So
**>>> please read the Help page on xyplot carefully and perhaps also
**>>> Deepayan's book on trellis graphics -- there are also undoubtedly
**>>> online resources: search on "trellis graphics tutorial" or some such.
**>>> This is not hard, but there are some details that you will need to
**>>> master,especially regarding argument passing.
**>>>
**>>> Another alternative is to use the layer() function in the latticeExtra
**>>> package instead. Consult the documentation there for details.
**>>>
**>>> Cheers,
**>>> Bert
**>>>
**>>>
**>>>
**>>> On Sun, Mar 6, 2011 at 5:17 AM, Umesh Rosyara <rosyaraur_at_gmail.com>
**>>> wrote:
**>>>> Dear Jorge, Dennis, Sarah and R-experts.
**>>>>
**>>>> Thank for helping me. As you mentioned it is difficult apply in
*

lattice

>>>> in

*>>>> this situation.
**>>>>
**>>>> Unless, there i
**>
**> --
**> Felix Andrews / 安福立
**> http://www.neurofractal.org/felix/
**>
**> ________________________________
**>
**> No virus found in this message.
**> Checked by AVG - www.avg.com
**> Version: 10.0.1204 / Virus Database: 1497/3495 - Release Date: 03/09/11
*

-- Felix Andrews / 安福立 http://www.neurofractal.org/felix/ _____ No virus found in this message. Checked by AVG - www.avg.com [[alternative HTML version deleted]] ______________________________________________ R-help_at_r-project.org 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 11 Mar 2011 - 12:17:09 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Fri 11 Mar 2011 - 12:30:20 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*