[R] alternate tick labels and tick marks with lattice xyplot

[Leah Marian]

Great, Thanks! This is really helpful!

On Thu, Jul 19, 2012 at 12:25 AM, ilai <keren at math.montana.edu> wrote:
> Maybe I'm missing something too but from your example seems like you are
> looking for
>
> xyplot(rnorm(12) ~ 1:12 , type="l",
> scales=list(x=list(at=seq(2,12,2),labels=c(1, ' ', 3 , ' ' , 5 , ' ' ))),
> par.settings=list(axis.components=list(bottom=list(tck=c(0,1)))))
>
> See "scales" in ?xyplot and str(trellis.par.get()) for some settings in
> lattice
>
> HTH
>
>
> On Wed, Jul 18, 2012 at 12:02 PM, Leah Marian <lmpreus at gmail.com> wrote:
>>
>> Yes,
>>
>> I would be interested in both the ggplot2 and lattice ways of doing
>> this. Unfortunately, I am not interested in creating a panel for each
>> chromosome. Actually, I would like to create a Manhattan plot using
>> xyplot. Thus I would need to alternate tick marks and tick labels.
>>
>> Thanks!
>>
>>
>>
>>
>> On Mon, Jul 16, 2012 at 12:11 PM, John Kane <jrkrideau at inbox.com> wrote:
>> >
>> > I have not seen any response yet so I thought I would reply.
>> >
>> > No idea of how to do this in lattice but an approximation of it can be
>> > done in ggplot2. I am trying to learn ggplot2 and it was a handy exercise.
>> > I still have not figured out how to get the extra line on the x-axis, hence
>> > the lines in the graph body instead
>> >
>> > Example:
>> > ##++++++++++++++++++++++++++++++++++++++++++++++++++++++++++###
>> >
>> > library(ggplot2)
>> > data  <-  structure(list(Chromosome = c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3,
>> > 3), BasePair = c(1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4), Pvalue =
>> > c(0.819178665755317,
>> > 0.462827404495329, 0.44360001408495, 0.871020796708763,
>> > 0.404167180880904,
>> > 0.115009917411953, 0.51048326632008, 0.292681957129389,
>> > 0.839718346949667,
>> > 0.586992112919688, 0.29609977430664, 0.873988818377256), indice = 1:12,
>> >     group = c("Group 1", "Group 2", "Group 1", "Group 1", "Group 1",
>> >     "Group 1", "Group 2", "Group 1", "Group 2", "Group 1", "Group 2",
>> >     "Group 2")), .Names = c("Chromosome", "BasePair", "Pvalue",
>> > "indice", "group"), row.names = c(NA, -12L), class = "data.frame")
>> >
>> > library(ggplot2)
>> >
>> > p  <-  ggplot(data, aes(indice, -log10(Pvalue))) + geom_line()  +
>> >           opts(legend.position = "none") +
>> >           scale_y_continuous(expression(paste(-log[10], "p-value"))) +
>> >           scale_x_continuous("Chromosome", breaks=c(2.5, 6.5 ,10.5),
>> > labels=c("1", "2","3")) +
>> >           geom_segment(aes(x = 4, y = 0.01, xend = 9, yend = 0.01,
>> > colour = group))  +
>> >           opts(title = "Results")  + facet_grid(. ~ group)
>> > p
>> >
>> > ##===========================================================##
>> > John Kane
>> > Kingston ON Canada
>> >
>> >
>> > > -----Original Message-----
>> > > From: lmpreus at gmail.com
>> > > Sent: Fri, 13 Jul 2012 15:33:43 -0400
>> > > To: r-help at r-project.org
>> > > Subject: [R] alternate tick labels and tick marks with lattice xyplot
>> > >
>> > > Hi,
>> > >
>> > > I would like to use xyplot to create a figure. Unfortunately, I cannot
>> > > find
>> > > documentation in xyplot to specify alternating the x-axis tick labels
>> > > with
>> > > the x-axis tick marks. I can do this with the regular R plot function
>> > > as
>> > > follows.
>> > >
>> > >
>> > > #A small version of my data looks like this
>> > > data<-data.frame(matrix(ncol=3,nrow=12))
>> > > data[,1]<-rep(c(1,2,3),c(4,4,4))
>> > > data[,2]<-rep(c(1,2,3,4),3)
>> > > data[,3]<-runif(12,0,1)
>> > > names(data)<-c("Chromosome", "BasePair", "Pvalue")
>> > > #using R's plot function, I would place the the chromosome label
>> > > between
>> > > the
>> > > #tick marks as follows:
>> > > v1<-c(4,8)
>> > > v2<-c(2,6,10)
>> > > data$indice<-seq(1:12)
>> > > plot(data$indice, -log10(data$Pvalue), type="l", xaxt="n",
>> > > main="Result",
>> > >  xlab="Chromosome", ylab=expression(paste(-log[10]," p-value")))
>> > > axis(1, v1,labels=FALSE )
>> > > axis(1, v2, seq(1:3), tick=FALSE, cex.axis=.6)
>> > >
>> > > Can this be done with lattice xyplot?
>> > >
>> > >
>> > > --
>> > > Leah Preus
>> > > Biostatistician
>> > > Roswell Park Cancer Institute
>> > >
>> > >       [[alternative HTML version deleted]]
>> > >
>> > > ______________________________________________
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>> > > https://stat.ethz.ch/mailman/listinfo/r-help
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>> > > http://www.R-project.org/posting-guide.html
>> > > and provide commented, minimal, self-contained, reproducible code.
>> >
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>>
>>
>> --
>> Leah Preus
>> Biostatistician
>> Roswell Park Cancer Institute
>>
>> ______________________________________________
>> 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.
>
>



-- 
Leah Preus
Biostatistician
Roswell Park Cancer Institute