[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

Tue Mar 8 06:00:27 CET 2011

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 is a possibility, I would try to use lattice. The major
>> reason
>> toward this is- my ultimate solution might be better of in lattice as I
>> have
>> a classificatory variable to make similar graph for each caterogory in the
>> lattice graph. Lattice cleates nice stacked xyplots.
>>
>> p ~ xvar | chr # require plots by the factor  variable "chr"
>>
>> # with a classificatory variable
>> 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 !
>> require(lattice)
>> xyplot(pval ~ xvar1|chr, dataf)
>>
>>
>> Best Regards
>>
>> Umesh R
>>
>>
>>
>>
>>  _____
>>
>> From: Jorge Ivan Velez [mailto:jorgeivanvelez at gmail.com]
>> Sent: Sunday, March 06, 2011 12:22 AM
>> To: Umesh Rosyara
>> Cc: R mailing list
>> Subject: Re: [R] displaying label meeting condition (i.e. significant,
>> i..e
>> p value less than 005) in plot function
>>
>>
>> Hi Umesh,
>>
>>
>> You can try something along the lines of:
>>
>>
>> d <- dataf[dataf$p < 0.05, ]   # p < 0.05
>> with(d, plot(xvar, p, col = 'white'))
>> with(d, text(xvar, p, name, cex = .7))
>>
>> HTH,
>> Jorge
>>
>>
>>
>> On Sat, Mar 5, 2011 at 12:29 PM, Umesh Rosyara <> wrote:
>>
>>
>> Dear R users,
>>
>> Here is my problem:
>>
>> # example data
>> name <- c(paste ("M", 1:1000, sep = ""))
>> xvar <- seq(1, 10000, 10)
>> set.seed(134)
>> p <- rnorm(1000, 0.15,0.05)
>> dataf <- data.frame(name,xvar, p)
>> plot (dataf$xvar,p)
>> abline(h=0.05)
>>
>> # I can know which observation number is less than 0.05
>> which (dataf$p < 0.05)
>> [1]  12  20  80 269 272 338 366 368 397 403 432 453 494 543 592 691 723
>> 789
>> 811
>> [20] 854 891 931 955
>>
>> I want to display (label) corresponding names on the plot above:
>> means that 12th observation M12, 20th observation M20 and so on. Please
>> note
>> that I have names not in numerical sequience (rather different names),
>> just
>> provided for this example to create dataset easily.
>>
>> Thanks in advance
>>
>> Umesh R
>>
>>
>>       [[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.
>>
>>
>>
>>  _____
>>
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>>
>>
>>        [[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.
>>
>
>
>
> --
> Bert Gunter
> Genentech Nonclinical Biostatistics
> 467-7374
> http://devo.gene.com/groups/devo/depts/ncb/home.shtml
>
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-- 
Bert Gunter
Genentech Nonclinical Biostatistics
467-7374
http://devo.gene.com/groups/devo/depts/ncb/home.shtml