Thank you for helping me and this solved the problem.... Best Regards Umesh R
_____ From: foolish.andr...@gmail.com [mailto:foolish.andr...@gmail.com] On Behalf Of Felix Andrews Sent: Friday, March 11, 2011 4:05 AM To: Umesh Rosyara Cc: R mailing list; deepayan.sar...@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 <rosyar...@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$p < 0.05)) > with(dataf[ok,], panel.text(p, xvar, name)) > }, as.table=T, subscripts=T) > > > Best Regards > > Umesh R > > > > > ________________________________ > From: foolish.andr...@gmail.com [mailto:foolish.andr...@gmail.com] On Behalf > Of Felix Andrews > Sent: Thursday, March 10, 2011 7:01 AM > To: Umesh Rosyara > Cc: R mailing list; deepayan.sar...@r-project.org > Subject: Re: [R] still a problem remainingRE: Data lebals xylattice plot: > RE: displaying label meeting condition (i.e. significant, i..e p value less > than 005) in plot function > > Notice that pvals is a subset of dataf so 'subscripts' can not be > applied directly to pvals. Instead you should do the subsetting inside > the panel function. e.g. > ok <- intersection(subscripts, which(dataf$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 <rosyar...@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.ber...@gene.com] >> Sent: Tuesday, March 08, 2011 12:00 AM >> To: Umesh Rosyara >> Cc: Jorge Ivan Velez; Dennis Murphy; sarah.gos...@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 <rosyar...@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.ber...@gene.com] >>> Sent: Sunday, March 06, 2011 10:50 AM >>> To: Umesh Rosyara >>> Cc: Jorge Ivan Velez; Dennis Murphy; sarah.gos...@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 <rosyar...@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. 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