From: Umesh Rosyara <rosyaraur_at_gmail.com>

Date: Thu, 10 Mar 2011 19:06:12 -0500

Date: Thu, 10 Mar 2011 19:06:12 -0500

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))

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 [[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 - 03:37:41 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 - 09:20:20 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.
*