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@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@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@gmail.com
> > > Sent: Fri, 13 Jul 2012 15:33:43 -0400
> > > To: r-help@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]]
> > >
> > > ______________________________________________
> > > 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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>
>
> --
> Leah Preus
> Biostatistician
> Roswell Park Cancer Institute
>
> ______________________________________________
> 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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