> -----Original Message-----
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Schwab,Wilhelm K
> Sent: Thursday, February 25, 2010 3:51 PM
> To: r-help@r-project.org
> Subject: [R] Ordering categories on a boxplot - a serious trap??
>
> Hello all,
>
> I think I probably did something stupid, and R's part was to
> allow me to do it. My goal was to control the order of
> factor levels appearing horizontally on a boxplot. Enter
> search engines and perhaps some creative stupidity on my
> part, and I came up with the following:
>
> v=read.table("factor-order.txt",header=TRUE);
> levels(v$doseGroup) = c("L", "M", "H");
> boxplot(v$dose~v$doseGroup);
levels<- translated the current level labels into
another language, it did not change the integer
codes of the factor. If you want to reorder the
levels call factor(..., levels=). E.g.,
> z <- factor(c("Small","Large","Medium","Small"))
> str(z)
Factor w/ 3 levels "Large","Medium",..: 3 1 2 3
> str(factor(z, levels=c("Small","Medium","Large")))
Factor w/ 3 levels "Small","Medium",..: 1 3 2 1
You can relabel them also by using the labels= argument
to factor
> str(factor(z, levels=c("Small","Medium","Large"),
labels=c("S","M","L")))
Factor w/ 3 levels "S","M","L": 1 3 2 1
Calling levels<- changes nothing but the level labels:
> zcopy <- z
> levels(zcopy) <- c("Small","Medium","Large")
> str(zcopy)
Factor w/ 3 levels "Small","Medium",..: 3 1 2 3
levels<- is handy for low-level manipulations but not
for general use. Even factor(,levels=) can be a bit
dangerous: if a new level is misspelled it will silently
add NA's to the data:
> str(factor(z, levels=c("Smal", "Medium", "Large")))
Factor w/ 3 levels "Smal","Medium",..: NA 3 2 NA
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
>
>
> A good way to see the trap is to evaluate:
>
> v=read.table("factor-order.txt",header=TRUE);
> par(mfrow=c(2,1));
> boxplot(v$dose~v$doseGroup);
> levels(v$doseGroup) = c("L", "M", "H");
> boxplot(v$dose~v$doseGroup);
> par(mfrow=c(1,1));
>
> The above creates two plots, one correct with the factors in
> an inconvient order, and one that is WRONG. In the latter,
> the labels appear in the desired order, but the data does not
> "move with them." I did not discover the problem until I
> repeated the same type of plot with something that had a
> known relationship with the levels, and the result was
> clearly not correct.
>
> I *think* the problem is to assign to the return value of
> levels(). How did I think to do that? I'm not really sure,
> but please look at
>
> https://stat.ethz.ch/pipermail/r-help/2008-August/171884.html
>
>
> Perhaps it does not say to do exactly what I did, but it sure
> was easy to follow to the mistake, it appeared to do what I
> wanted, and the consequences of the mistake are ugly.
> Perhaps levels() should return something that is immutable??
> If I am looking at this correctly, levels() is an accident
> waiting to happen.
>
> What should I have done? It seems:
>
> read data and order factor levels
> v=read.table("factor-order.txt",header=TRUE);
> group = factor(v$doseGroup,levels = c("L", "M", "H") );
> boxplot(v$dose~group);
>
>
> One disappointment is that the above factor() call apparently
> needs to be repeated for any subset of v - I'm still trying
> to get my mind around that one.
>
> Can anyone confirm this? It strikes me as a trap that should
> be addressed so that an error results rather than a garbage graph.
>
> Bill
>
>
> ---
> Wilhelm K. Schwab, Ph.D.
>
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