Dear Charles,
the sample code you cite has an additional "as.dendrogram" compared to
your code. Hence, dend1 is of class dendrogram (class(dend1)) and if you
call plot(dend1) the method for dendrograms (i.e., plot.dendrogram) is
executed which has a horiz argument; confer ?plot.dendrogram.
Whereas in your code h is of class hclust (class(hclust)) and therefore
plot(h) leads to a call of plot.hclust which has no horiz argument; cf.
?plot.hclust.
So, adding as.dendrogram in your code should remove the warning messages
and give what you want; e.g.
plot(as.dendrogram(h), horiz = TRUE)
Best,
Matthias
Charles K. Minns wrote:
I am using hclust and plot to produce dendrograms. Using my input data I am
able to complete an analysis and obtain a vertical plot.
I want to be able to plot the dendrogram horizontally.I am using version 2.6
of R and have updated my packages recently.
Using the sample script for dendrograms I can produce a horizontal plot
using the instruction horiz = TRUE in plot().
When I use the same instruction in my own script I get a warning message
that horiz, and horizontal, are not recognized commands in plot.
I cannot find any documentation in R on how to change the orientation of
plots and general searches for information on this subject.
Can someone explain why my script does not work.
Sample code follows:
-----------------------------------------------------------------------
# Sample code extracted from the Dendrogram documentation in R
#
require(graphics); require(utils)
hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc)) # "print()" method
str(dend1) # "str()" method
str(dend1, max = 2) # only the first two sub-levels
op <- par(mfrow= c(2,2), mar = c(5,2,1,4))
plot(dend1, horiz = TRUE)
plot(dend1)
#
# My code
#
x <- read.table("Rclust2.data",header=TRUE)
m <- data.matrix(x)
d <- as.dist(m)
h <- hclust(d)
plot(h, horiz = TRUE)
----------------------------------------------------------------------
The three plot commands execute. Plot 1 is horizontal, plot 2 is vertical
and plot 3 is vertical. Plus plot 3
generates the console output:
-----------------------------------------------------------------
#
# My code
#
x <- read.table("Rclust2.data",header=TRUE)
m <- data.matrix(x)
d <- as.dist(m)
h <- hclust(d)
plot(h, horiz = TRUE)
Warning messages:
1: In plot.hclust(h, horiz = TRUE) : "horiz" is not a graphical parameter
2: In plot.hclust(h, horiz = TRUE) : "horiz" is not a graphical parameter
3: In title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
"horiz" is not a graphical parameter
---------------------------------------------------------------
I would appreciate help solving this problem. Doubtless there is a simple
answer.
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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
