[R] Generate Dendrogram

[cberry at tajo.ucsd.edu]

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