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

From: Umesh Rosyara <rosyaraur_at_gmail.com>
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/
>
> ________________________________
>
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--
Felix Andrews / 安福立
http://www.neurofractal.org/felix/ 

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