[R] Problem with data frame when using xYplot?

Sander Oom slist at oomvanlieshout.net
Fri May 13 15:07:43 CEST 2005 

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 at oomvanlieshout.net
Web     www.oomvanlieshout.net/sander

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