[R] 2D cluster of 2D matrix in R?

Mark Wall wall at chop.swmed.edu
Fri Apr 19 22:26:06 CEST 2002


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 

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
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