On Jan 11, 2011, at 9:27 PM, David Winsemius wrote:
On Jan 11, 2011, at 7:01 PM, Richard Vlasimsky wrote:
Has anyone successfully created a PNG file for a dendrogram?
I am able to successfully launch and view a dendrogram in Quartz.
However, the dendrogram is quite large (too large to read on a
computer screen), so I am trying to save it to a file (1000x4000
pixels) for viewing in other apps. However, whenever I try to
initiate a PNG device, I get a "need finitite 'xlim' values" error.
Here is some example code to illustrate my point:
cor.matrix <-
cor(mydata,method="pearson",use="pairwise.complete.obs");
distance <- as.dist(1.0-cor.matrix);
hc <- hclust(distance);
p <- plot(hc);
plot(p);
#This works! Plot is generated in quartz no problem.
#Now, try this:
png(filename="delme.png",width=4000,height=1000);
cor.matrix <-
cor(mydata,method="pearson",use="pairwise.complete.obs");
distance <- as.dist(1.0-cor.matrix);
hc <- hclust(distance);
p <- plot(hc);
plot(p);
#Error in plot.window(...) : need finite 'xlim' values
#In addition: Warning messages:
#1: In min(x) : no non-missing arguments to min; returning Inf
#2: In max(x) : no non-missing arguments to max; returning -Inf
#3: In min(x) : no non-missing arguments to min; returning Inf
#4: In max(x) : no non-missing arguments to max; returning -Inf
I'm not sure the other two answers address the problems I found.
When I try to set up a png file with the parameters
width=4000,height=1000, on a Mac I intially got no plot with what is
an otherwise valid command. But after successfully getting plotting
to a png device the logjam appear broken. Try:
graphics.off()
dev.list()
#NULL
png(filename="delme.png",width=4000,height=1000);
plot(hc)
dev.off()
(Of course I used dev.off() which you did not, but even adding
dev.off() was not enough to get success, at least initially. I don't
understand the suggestion to get rid of plot(hc) or the suggestion
that hclust() returns NULL. That's certainly not how I read the help
page and examples for hclust.)
I guess it's true to say that I misunderstood when Venables and
Langfelder _didn't_ say either of those things. They said that
plot(plot(hc)) was not needed and I have now seen the light. The
missing ingredient in the OP's frustrations is still dev.off().
This is the exact same code, only a prior call to png() causes the
seemingly unrelated xlim to fail. Why is this?
Thanks,
Richard Vlasimsky
David Winsemius, MD
West Hartford, CT
David Winsemius, MD
West Hartford, CT
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