Leah Marian
2012-Jul-13 19:33 UTC
[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]]
Leah Marian
2012-Jul-18 18:02 UTC
[R] alternate tick labels and tick marks with lattice xyplot
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]] > > > > ______________________________________________ > > 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. > > ____________________________________________________________ > 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
John Kane
2012-Jul-18 20:22 UTC
[R] alternate tick labels and tick marks with lattice xyplot
Oh, I clearly misunderstood what you were doing there. I don't know anything about Manhattan plots but a quick google for "manhattan plot r package" turns up a number of items so the type of plot you want may already exist. Sorry to not be of more help. John Kane Kingston ON Canada> -----Original Message----- > From: lmpreus at gmail.com > Sent: Wed, 18 Jul 2012 14:02:49 -0400 > To: jrkrideau at inbox.com > Subject: Re: [R] alternate tick labels and tick marks with lattice xyplot > > 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]] >>> >>> ______________________________________________ >>> 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. >> >> ____________________________________________________________ >> 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____________________________________________________________ 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