[R] Generate Dendrogram

[Mercier Eloi]

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