R help - May 2013 - Error in plot.window(...) : need finite 'xlim' values

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)

	[[alternative HTML version deleted]]

On 05.05.2013 14:20, 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 :)

Please see the positng guide that asks for reproducible code.Yours is 
not since we have no "J:/research/source/treePhone_binary.csv".

Best,
Uwe Ligges

> 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)
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org 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.
>

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