Re: [R] Problem with data frame when using xYplot?

From: Sander Oom <slist_at_oomvanlieshout.net>
Date: Sat 14 May 2005 - 01:15:31 EST

I have edited the code (hacked from another graph) to provide more control over the different elements of the graph. Now we have a graph at publication quality! Slowly the power of R graphics is shining through the thick cloud of options! Beautiful.


library(Hmisc)
library(lattice)

ltheme <- canonical.theme(color = FALSE)     ## in-built B&W theme
ltheme$strip.background$col <- "transparent" ## change strip bg
lattice.options(default.theme = ltheme)      ## set as default
tmp <-
structure(list(Position = structure(as.integer(c(1, 2, 1, 2, 1, 2, 1, 2)), .Label = c("Inside", "Outside"), class = "factor"),

     AltGeo = structure(as.integer(c(1, 1, 2, 2, 3, 3, 4, 4)), .Label = c("Basalt-High",

     "Basalt-Low", "Quartz-High", "Quartz-Low"), class = "factor"),
     Sodium = c(27.3333333333333, 26.8888888888889, 25, 18.1111111111111,
     4.66666666666667, 5.55555555555556, 10.6666666666667, 5.66666666666667
     ), SD = c(5.3851648071345, 2.42097317438899, 20.1618451536560,
     15.2679766541317, 5.45435605731786, 8.09492296305393, 10.6183802907976,
     8.06225774829855), Nobs = c(9, 9, 9, 9, 9, 9, 9, 9), Lower = 
c(25.5382783976218,
     26.0818978307592, 18.2793849487813, 13.0217855597339, 2.84854798089405,
     2.85724790120425, 7.12720656973412, 2.97924741723382), Upper = 
c(29.1283882690448,
     27.6958799470186, 31.7206150512187, 23.2004366624884, 6.48478535243929,
     8.25386320990686, 14.2061267635992, 8.35408591609952)), .Names = 
c("Position",
"AltGeo", "Sodium", "SD", "Nobs", "Lower", "Upper"), row.names = c("1", "2", "3", "4", "5", "6", "7", "8"), class = "data.frame") tmp$xvar <- rep(1:4, each=2)+rep(c(-.05,.05), 4) tmp
sp <- list(superpose.symbol = list(pch = c(16,1), cex = 1)) xYplot(Cbind(Sodium,Lower,Upper) ~ xvar, groups=Position, data=tmp,
     scales=list(y='free',x=list(at=1:4, labels=levels(tmp$AltGeo))),
     xlim=c(0.5, 4.5), ylim=c(min(tmp$Lower)-1,max(tmp$Upper)+1),
     xlab='AltGeo', ylab='Sodium',
         panel = function(x, y, type, ...) {
           panel.xYplot(x, y, type="p",...)
           lpoints(x, y, pch=16, col="white", cex=2)
           panel.superpose(x, y, type="p", ...)
         },
         par.settings = sp,
     auto.key=list(columns=1, x=0.7, y=0.8, corner = c(0,0))
     )

********************


Sander Oom wrote:
> An off list response from Mat Soukop (thanks Mat!!) provides an even
> more elegant solution (see code below)! I have included the original
> code, so people can decide whether to plot in a single panel or in
> multiple panels. Now we have a fully functional workaround to get
> plotmeans{gplots} for multiple factors using lattice! Great!
>
> ********************
>
>
> library(Hmisc)
> library(lattice)
> tmp <-
> structure(list(Position = structure(as.integer(c(1, 2, 1, 2,
> 1, 2, 1, 2)), .Label = c("Inside", "Outside"), class = "factor"),
> AltGeo = structure(as.integer(c(1, 1, 2, 2, 3, 3, 4, 4)), .Label =
> c("Basalt-High",
> "Basalt-Low", "Quartz-High", "Quartz-Low"), class = "factor"),
> Sodium = c(27.3333333333333, 26.8888888888889, 25, 18.1111111111111,
> 4.66666666666667, 5.55555555555556, 10.6666666666667, 5.66666666666667
> ), SD = c(5.3851648071345, 2.42097317438899, 20.1618451536560,
> 15.2679766541317, 5.45435605731786, 8.09492296305393, 10.6183802907976,
> 8.06225774829855), Nobs = c(9, 9, 9, 9, 9, 9, 9, 9), Lower =
> c(25.5382783976218,
> 26.0818978307592, 18.2793849487813, 13.0217855597339, 2.84854798089405,
> 2.85724790120425, 7.12720656973412, 2.97924741723382), Upper =
> c(29.1283882690448,
> 27.6958799470186, 31.7206150512187, 23.2004366624884, 6.48478535243929,
> 8.25386320990686, 14.2061267635992, 8.35408591609952)), .Names =
> c("Position",
> "AltGeo", "Sodium", "SD", "Nobs", "Lower", "Upper"), row.names = c("1",
> "2", "3", "4", "5", "6", "7", "8"), class = "data.frame")
> tmp$PosNum <- unclass(tmp$Position)
> tmp
> (labs <- unique(tmp$Position))
> # plot factor levels in seperate panels
> xYplot(Cbind(Sodium,Lower,Upper) ~ PosNum|AltGeo, data=tmp, nx=FALSE,
> xlim=c(0.5,2.5),
> ylim=c(min(tmp$Lower)-1,max(tmp$Upper)+1),
> scales = list(x = list(at=seq(1, 2, by=1), labels = labs)),
> xlab="Position", ylab="Sodium"
> )
>
> ################
> new.back <- trellis.par.get("background")
> new.back$col <- "white"
> newcol <- trellis.par.get("superpose.symbol")
> newcol$col <- c('green4','blue','red','black')
> newcol$pch <- c(16,1,4,8)
> new.line <- trellis.par.get("box.rectangle")
> new.line$col <- 'black'
> trellis.par.set("background", new.back)
> trellis.par.set("superpose.symbol", newcol)
> trellis.par.set("box.rectangle", new.line)
> # Plot factor levels in one graph
> tmp$xvar <- rep(1:4, each=2)+rep(c(-.05,.05), 4)
> xYplot(Cbind(Sodium,Lower,Upper) ~ xvar, groups=Position, data=tmp,
> scales=list(y='free',x=list(at=1:4,
> labels=levels(tmp$AltGeo))),
> xlab='AltGeo', xlim=c(.5, 4.5),
> key=list(points=Rows(trellis.par.get("superpose.symbol"),1:2),
> text=list(lab =as.character(levels(tmp$Position)),
> col=trellis.par.get("superpose.symbol")$col[1:2]),
> columns=2, cex=1, title="Position",
> cex.title=1.1))
>
>
> ********************
>
>
> Sander Oom wrote:

>> Problem solved!
>>
>> I was so focused on reproducing the plotmeans() functionality with 
>> xYplot() that I completely overlooked the fact that my data does not 
>> allow a x-y plot, as only Sodium is a numeric variable while Position 
>> and AltGeo are factors!
>>
>> Using unclass() to make Position a numeric variable does the trick:
>> tmp$Position <- unclass(tmp$Position)
>>
>> The code below does the trick. Now I only need to figure out how to 
>> tweak the x axis to pretend I am plotting a factor, i.e. plotting 
>> labels "Inside" and "Outside".
>>
>> Cheers,
>>
>> Sander.
>>
>>
>> library(Hmisc)
>> library(Lattice)
>> tmp <-
>> structure(list(Position = structure(as.integer(c(1, 2, 1, 2,
>> 1, 2, 1, 2)), .Label = c("Inside", "Outside"), class = "factor"),
>>     AltGeo = structure(as.integer(c(1, 1, 2, 2, 3, 3, 4, 4)), .Label = 
>> c("Basalt-High",
>>     "Basalt-Low", "Quartz-High", "Quartz-Low"), class = "factor"),
>>     Sodium = c(27.3333333333333, 26.8888888888889, 25, 18.1111111111111,
>>     4.66666666666667, 5.55555555555556, 10.6666666666667, 
>> 5.66666666666667
>>     ), SD = c(5.3851648071345, 2.42097317438899, 20.1618451536560,
>>     15.2679766541317, 5.45435605731786, 8.09492296305393, 
>> 10.6183802907976,
>>     8.06225774829855), Nobs = c(9, 9, 9, 9, 9, 9, 9, 9), Lower = 
>> c(25.5382783976218,
>>     26.0818978307592, 18.2793849487813, 13.0217855597339, 
>> 2.84854798089405,
>>     2.85724790120425, 7.12720656973412, 2.97924741723382), Upper = 
>> c(29.1283882690448,
>>     27.6958799470186, 31.7206150512187, 23.2004366624884, 
>> 6.48478535243929,
>>     8.25386320990686, 14.2061267635992, 8.35408591609952)), .Names = 
>> c("Position",
>> "AltGeo", "Sodium", "SD", "Nobs", "Lower", "Upper"), row.names = c("1",
>> "2", "3", "4", "5", "6", "7", "8"), class = "data.frame")
>> tmp$Position <- unclass(tmp$Position)
>> xYplot(Cbind(Sodium,Lower,Upper) ~ Position|AltGeo, groups=AltGeo,
>>   data=tmp, ylim=c(min(tmp$Lower)-1,max(tmp$Upper)+1),
>>   xlab="Position", ylab="Sodium"
>>   )
>>
>>
>>
>> Sander Oom wrote:
>>> Dear all,
>>>
>>> I am trying to plot means and error bars using xYplot, but I get an 
>>> error message from xYplot which I can not figure out:
>>>  > Error in Summary.factor(..., na.rm = na.rm) :
>>>         range not meaningful for factors
>>>
>>> The data frame (tmpNa) was created using aggregate. I have used dump 
>>> to created the code below, which generates the same error.
>>>
>>> Can anybody tell me what is wrong with the data frame?
>>>
>>> Thanks in advance,
>>>
>>> Sander.
>>>
>>> library(Hmisc)
>>> tmpNa <-
>>> structure(list(Position = structure(as.integer(c(1, 2, 1, 2,
>>> 1, 2, 1, 2)), .Label = c("Inside", "Outside"), class = "factor"),
>>>     AltGeo = structure(as.integer(c(1, 1, 2, 2, 3, 3, 4, 4)), .Label 
>>> = c("Basalt-High",
>>>     "Basalt-Low", "Quartz-High", "Quartz-Low"), class = "factor"),
>>>     Sodium = c(27.3333333333333, 26.8888888888889, 25, 18.1111111111111,
>>>     4.66666666666667, 5.55555555555556, 10.6666666666667, 
>>> 5.66666666666667
>>>     ), SD = c(5.3851648071345, 2.42097317438899, 20.1618451536560,
>>>     15.2679766541317, 5.45435605731786, 8.09492296305393, 
>>> 10.6183802907976,
>>>     8.06225774829855), Nobs = c(9, 9, 9, 9, 9, 9, 9, 9), Lower = 
>>> c(25.5382783976218,
>>>     26.0818978307592, 18.2793849487813, 13.0217855597339, 
>>> 2.84854798089405,
>>>     2.85724790120425, 7.12720656973412, 2.97924741723382), Upper = 
>>> c(29.1283882690448,
>>>     27.6958799470186, 31.7206150512187, 23.2004366624884, 
>>> 6.48478535243929,
>>>     8.25386320990686, 14.2061267635992, 8.35408591609952)), .Names = 
>>> c("Position",
>>> "AltGeo", "Sodium", "SD", "Nobs", "Lower", "Upper"), row.names = c("1",
>>> "2", "3", "4", "5", "6", "7", "8"), class = "data.frame")
>>> xYplot(Cbind(Sodium,Lower,Upper) ~ AltGeo, groups=Position,  data=tmpNa)
>>>
>>>
>>>  > version
>>>          _
>>> platform i686-pc-linux-gnu
>>> arch     i686
>>> os       linux-gnu
>>> system   i686, linux-gnu
>>> status
>>> major    2
>>> minor    1.0
>>> year     2005
>>> month    04
>>> day      18
>>> language R
>>>
>>

>
-- 
--------------------------------------------
Dr. Sander P. Oom
Animal, Plant and Environmental Sciences,
University of the Witwatersrand
Private Bag 3, Wits 2050, South Africa
Tel (work)      +27 (0)11 717 64 04
Tel (home)      +27 (0)18 297 44 51
Fax             +27 (0)18 299 24 64
Email   sander@oomvanlieshout.net
Web     www.oomvanlieshout.net/sander

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Received on Sat May 14 01:21:45 2005

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