Problem with data frame when using xYplot?
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