From: Marc Schwartz <marc_schwartz_at_comcast.net>

Date: Fri 26 Jan 2007 - 17:46:23 GMT

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat Jan 27 04:50:22 2007

Date: Fri 26 Jan 2007 - 17:46:23 GMT

On Fri, 2007-01-26 at 11:50 -0500, Michael Rennie wrote:

> Hi, there

*>
**> I'm trying to plot what is returned from a call to tapply, and can't figure
**> out how to do it. My guess is that it has something to do with the
**> inclusion of row names when you ask for the values you're interested in,
**> but if anyone has any ideas on how to get it to work, that would be
**> stellar. Here's some example code:
**>
**> y1<-rnorm(40, 2)
**> x1<-rep(1:2, each=20)
**> x2<-rep(1:2, each=10 times=2)
**>
**> ex.dat<-data.frame(cbind(y1,x1,x2))
**>
**> ex.dat$x1<-factor(ex.dat$x1, labels=c("A", "B"))
**> ex.dat$x2<-factor(ex.dat$x2, labels=c("C", "D"))
**>
**> attach(ex.dat)
**>
**> xbar<-tapply(ex.dat$y1, ex.dat[,-1], mean)
**> xbar
**>
**> #values I'd like to plot:
**> row.names(xbar) #levels of x1
**> xbar[,1] #mean response of y1 for group C (x2) across x1
**>
**> #plot mean response y1 for group C against x1 (i.e., using x2 as a grouping
**> factor).
**> plot(row.names(xbar), xbar[,1], ylim=range[y1])
**>
**> #This is where things break down. The error message states that I need
**> "finite xlim values" but I haven't assigned anything to xlim. If I just
**> plot the data:
**>
**> plot(x1, y1)
**>
**> #This works fine.
**>
**> #And, I can get this to work:
**>
**> stripchart(xbar[1,]~row.names(xbar), vert=T)
**>
**> #However, I'd like to then add the values for the second set of means
**> (i.e., mean values for group D against x1, or (xbar[,2])) to the plot.
**> #I tried following up the previous command with:
**>
**> points(row.names(xbar), xbar[,2])
**>
**> #But that returns an error as well (NAs introduced by coercion).
**>
**>
**>
**> Any suggestions?
**>
**> Cheers,
**>
**> Mike
**>
**> PS- some of you might suggest for me to use interaction.plot, since this is
**> essentially what I'm building here. True, but I can't get error bars using
**> interaction.plot. I'm therefore trying to build my own version where I can
**> specify the inclusion of error bars. Presumably the interaction.plot has
**> figured out how to do what I'm attempting, so I have some faith that I am
**> on the right track....
*

Michael,

The problem is that when you are using the rownames for 'xbar', they are a character vector:

> str(rownames(xbar))

chr [1:2] "A" "B

When you attempt to use the same values from 'ex.dat$x1', they are factors, which are being coerced to their numeric equivalents, so that they can work as x axis values.

> str(ex.dat$x1)

Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ...

> as.numeric(ex.dat$x1)

[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[35] 2 2 2 2 2 2

I might note using the following:

par(mfcol = c(1, 3))

with(ex.dat, plot(1:2, xbar[, 1], ylim = range(y1),

type = "b", col = "red", lty = c("dashed", "solid"), xaxt = "n", xlab = "x1", ylab = "mean of y1")) with(ex.dat, points(1:2, xbar[, 2], col = "blue", type = "b"))

axis(1, at = 1:2, labels = c("A", "B"))

matplot(1:2, xbar, col = c("red", "blue"),

pch = 21, type = "b", ylim = range(y1), lty = c("dashed", "solid"), xaxt = "n", xlab = "x1", ylab = "mean of y1")

axis(1, at = 1:2, labels = c("A", "B"))

with(ex.dat, interaction.plot(x1, x2, response = y1,

type = "b", pch = 21, col = c("red", "blue"), ylim = range(ex.dat$y1), legend = FALSE))

You get basically the same 3 plots, with the principal difference in interaction.plot() being a different x axis range.

Using interaction.plot(), you can get the proper basic plot and then add the CI's if you wish, since you know the x axis values of the mean estimates, which is 1:NumberOfGroups (as in a boxplot).

interaction.plot() actually uses matplot() internally.

**HTH,
**
Marc Schwartz

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