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 <lmpr...@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 <jrkrid...@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: lmpr...@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. > > > > ____________________________________________________________ > > GET FREE SMILEYS FOR YOUR IM & EMAIL - Learn more at > http://www.inbox.com/smileys > > Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk > and most webmails > > > > > > > > -- > 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. > [[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.