On 05/05/2013 10:20 PM, shaqifahsani wrote:
Hi,
I am very new to R. I am planning to plot a dendrogram from a binary file
but received error after running it. I retrieved the code from the Internet
and customized it accordingly...
Error: Error in plot.window(...) : need finite 'xlim' values
Can you explain why and what should I do... Thank you :)
code:
# load required libraries
library(cluster) # clustering functions
library(ape) # plotting
# retrieve csv data
treePhone<- read.csv("J:/research/source/treePhone_binary.csv")
# combine into single data.frame
df_treePhone<- data.frame(treePhone)
d_treePhone<- daisy(df_treePhone)
# perform divisive hierarcical clustering for dendrogram creation
di_treePhone.diana<- diana(d_treePhone)
# convert object into 'phylo' class for plotting
p_treePhone.phylo<- as.phylo(as.hclust(di_treePhone.diana))
# plot dendrogram representation, annotated with the same labels
plot(p_treePhone.phylo)
Hi shaqifahsani,
This is almost certainly due to missing values in the final data
structure "p_treePhone.phylo" (which may have propagated from missing
values in the original data frame). I think that p_treePhone.phylo will
probably have "x" and "y" components. You can see the structure with:
str(p_treePhone.phylo)
If there is a "$x" component, look at it with:
p_treePhone$x
If there are any NA or NaN or Inf values, this is your problem. You may
be able to get around it with the "complete.cases" function.
Jim
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