[R] Problem with data frame when using xYplot?
Sander Oom
slist at oomvanlieshout.net
Fri May 13 17:15:31 CEST 2005
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 at oomvanlieshout.net
Web www.oomvanlieshout.net/sander
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