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 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:jorgeivanve...@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@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@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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