From: Mark Wall (wall@chop.swmed.edu)
Date: Sat 20 Apr 2002 - 06:26:06 EST
Message-id: <a05101001b8e62cde7200@[129.112.5.53]>
Hello!
I would love to use R for the following 2 tasks, but am unable to
determine if R is well suited for this. My primary question- is this
possible in R? Secondary- if yes, how?
We routinely use MatLab with the Statistics Tool Box to manipulate
and plot a 2 dimensional matrix (m x n) of real numbers. If you
think of each dimension as an array of vectors (e.g. a collection of
m vectors (each n-dimensions), we 1) cluster these (and generate a
dendrogram) for both dimensions as below using a city-block distance
measure:
original matrix with labels
----------------
W X Y Z
A 0 1 0 0
B 0 1 0 1
C 5 0 0 0
D 0 0 0 2
E 5 0 0 0
Clustered matrix
----------------
W Y X Z
E 5 0 0 0
C 5 0 0 0
A 0 0 1 0
B 0 0 1 1
D 0 0 0 2
In reality, m and n are between 50 and 1000 so we 2) display these
matrices as an x-y-color plot for easy visualization. Think of this
as a square frame with each pixel representing a matrix element. The
values are represented by a continuous color scale (dark blue = low
values, through yellow to red = high values). I can provide a JPEG
if necessary.
With large matrices, we isolate sub-clusters by creating new matrices
that are the appropriate slices of the original matrix and then
repeat steps 1 and 2 for each sub-cluster.
Thank you,
Mark Wall
---------
HHMI/UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, Texas 75390-9050
USA
214.648.5050
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