R help - Apr 2012 - Generate Dendrogram

Hi

I have a distance matrix which is computed by user defined method. I 
would like to plot the dendrogram. I would like to use different color 
and want the leaves laying down bottom.
The script like this. I am not familiar with R. I followed the example 
shown in 
http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html

dist.obj <- as.dist(matrix.distance)
hc.obj <- hclust(dist.obj,method="ave")
dend1 <- as.dendrogram(hc.obj)
plot(hc.obj, xlab='',ylab='',sub='', nodePar=list(pch =
c(1,NA),
cex=0.8, lab.cex = 0.8)).

But I got warning and the plot does not look like what I wanted.

Warning messages:
In plot.hclust(hc.obj, xlab = "", ylab = "", sub =
"", nodePar =
list(pch = c(1,  :
   "nodePar" is not a graphical parameter

It also can not recognize

edgePardLeafedge.root

Does someone know what's wrong?

Br,
Luffy

farscape2012 <farscape2012 at live.com> writes:
> Hi
>
> I have a distance matrix which is computed by user defined method. I
> would like to plot the dendrogram. I would like to use different color
> and want the leaves laying down bottom.
> The script like this. I am not familiar with R. I followed the example
> shown in
> http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html
>
> dist.obj <- as.dist(matrix.distance)
> hc.obj <- hclust(dist.obj,method="ave")
> dend1 <- as.dendrogram(hc.obj)
> plot(hc.obj, xlab='',ylab='',sub='',
nodePar=list(pch = c(1,NA),
> cex=0.8, lab.cex = 0.8)).
>
> But I got warning and the plot does not look like what I wanted.
>
> Warning messages:
> In plot.hclust(hc.obj, xlab = "", ylab = "", sub =
"", nodePar > list(pch = c(1,  :
>   "nodePar" is not a graphical parameter
>
> It also can not recognize
>
> edgePar> dLeaf> edge.root
>
> Does someone know what's wrong?

Yep. You did not follow the example.

You used the wrong object in the call to plot() and it dispatched to
plot.hclust rather than plot.dendrogram.

Try 

    plot( dend1, ... )

HTH,

Chuck

>
> Br,
> Luffy
>
-- 
Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at ucsd edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

hc.obj is not a dendrogram.

plot(dend1, xlab='',ylab='',sub='', nodePar=list(pch =
c(1,NA), cex=0.8,
lab.cex = 0.8))

See ?plot.hclust and ?plot.dendrogram. They are not using the same 
arguments.

Regards,

Eloi


On 12-04-30 06:36 AM, farscape2012 wrote:
> Hi
>
> I have a distance matrix which is computed by user defined method. I 
> would like to plot the dendrogram. I would like to use different color 
> and want the leaves laying down bottom.
> The script like this. I am not familiar with R. I followed the example 
> shown in 
> http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html
>
> dist.obj <- as.dist(matrix.distance)
> hc.obj <- hclust(dist.obj,method="ave")
> dend1 <- as.dendrogram(hc.obj)
> plot(hc.obj, xlab='',ylab='',sub='',
nodePar=list(pch = c(1,NA),
> cex=0.8, lab.cex = 0.8)).
>
> But I got warning and the plot does not look like what I wanted.
>
> Warning messages:
> In plot.hclust(hc.obj, xlab = "", ylab = "", sub =
"", nodePar =
> list(pch = c(1,  :
>   "nodePar" is not a graphical parameter
>
> It also can not recognize
>
> edgePar> dLeaf> edge.root
>
> Does someone know what's wrong?
>
> Br,
> Luffy
>
> ______________________________________________
> 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.
>

-- 
Eloi Mercier
Bioinformatics PhD Student, UBC
Paul Pavlidis Lab
2185 East Mall
University of British Columbia
Vancouver BC V6T1Z4