[R] plot.hclust with lots of objects

[Martin Maechler]

>>>>> "TP" == Thomas Petzoldt <thpe at simecol.de>
>>>>>     on Sat, 08 Nov 2008 11:11:30 +0100 writes:

    TP> Hi Paul, one possibility: write the tree to a wide pdf
    TP> file and then zoom and scroll using Adobe Acrobat or
    TP> another PDF reader. Here is a tree with 1000 objects:

    TP> x <- matrix(rnorm(3000), nrow=1000)
    TP> hc <- hclust(dist(x))
    TP> pdf("tree.pdf", width=150)
    TP> plot(hc)
    TP> dev.off()

Indeed.
Also,  if you first transform your  hclust()  result into a "dendrogram"
i.e.
  dhc <- as.dendrogram(hc)
  ...
  plot(dhc, ......)

you can make use of the (hidden!) plot.dendrogram() method
which is much more customizable (but typically slower)
than plot.hclust().

Martin Maechler, ETH Zurich



    TP> paul murima wrote:
    >> Dear all,
    >> 
    >> The default plotting method for hclust trees looks just fine for few
    >> objects like in the example dataset. But when it comes to many
    >> features (eg some 1000 and more - I'm trying to visualize clustered
    >> microarray data) it renders a tree, that one cannot inspect, because
    >> of overlapping text and lines. My question is, is there a way or a
    >> plotting parameter for plotting a tree which is wide enough to have
    >> all leaves separated and readable labels even for that many objects?
    >> This would produce a very big image, so I think scrolling is
    >> essential.
    >> 
    >> I believe the answer is simple, but I'm unable to figure it out.
    >> 
    >> Thanks in advance
    >> 
    >> --
    >> BEST
    >> 
    >> Paul Murima
    >> 
    >> ______________________________________________
    >> R-help at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-help
    >> PLEASE do read the posting guide 
    TP> http://www.R-project.org/posting-guide.html
    >> and provide commented, minimal, self-contained, reproducible code.


    TP> -- 
    TP> Thomas Petzoldt
    TP> Technische Universitaet Dresden
    TP> Institut fuer Hydrobiologie        thomas.petzoldt at tu-dresden.de
    TP> 01062 Dresden                      http://tu-dresden.de/hydrobiologie/
    TP> GERMANY

    TP> ______________________________________________
    TP> R-help at r-project.org mailing list
    TP> https://stat.ethz.ch/mailman/listinfo/r-help
    TP> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    TP> and provide commented, minimal, self-contained, reproducible code.

    TP> x <- matrix(rnorm(3000), nrow=1000) hc <-
    TP> hclust(dist(x)) pdf("tree.pdf", width=150) plot(hc)
    TP> dev.off()


    TP> Thomas P.


    TP> paul murima wrote:
    >> Dear all,
    >> 
    >> The default plotting method for hclust trees looks just
    >> fine for few objects like in the example dataset. But
    >> when it comes to many features (eg some 1000 and more -
    >> I'm trying to visualize clustered microarray data) it
    >> renders a tree, that one cannot inspect, because of
    >> overlapping text and lines. My question is, is there a
    >> way or a plotting parameter for plotting a tree which is
    >> wide enough to have all leaves separated and readable
    >> labels even for that many objects?  This would produce a
    >> very big image, so I think scrolling is essential.
    >> 
    >> I believe the answer is simple, but I'm unable to figure
    >> it out.
    >> 
    >> Thanks in advance
    >> 
    >> --
    >> BEST
    >> 
    >> Paul Murima
    >> 
    >> ______________________________________________
    >> R-help at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
    >> read the posting guide
    TP> http://www.R-project.org/posting-guide.html
    >> and provide commented, minimal, self-contained,
    >> reproducible code.


    TP> -- Thomas Petzoldt Technische Universitaet Dresden
    TP> Institut fuer Hydrobiologie
    TP> thomas.petzoldt at tu-dresden.de 01062 Dresden
    TP> http://tu-dresden.de/hydrobiologie/ GERMANY

    TP> ______________________________________________
    TP> R-help at r-project.org mailing list
    TP> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
    TP> read the posting guide
    TP> http://www.R-project.org/posting-guide.html and provide
    TP> commented, minimal, self-contained, reproducible code.