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

[John Kane]

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]]
>>> 
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>>> http://www.R-project.org/posting-guide.html
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>> 
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> 
> 
> --
> Leah Preus
> Biostatistician
> Roswell Park Cancer Institute

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