Hi all,
I have a distance matrix (symmetric) which looks somewhat like this (only a
small portion shown)
ENSG00000101413 ENSG00000176884 ENSG00000185532 ENSG00000106829
ENSG00000101413 1.000 1.000 1.000 1.000
ENSG00000176884 0.328 0.258 0.260 0.390
ENSG00000185532 1.000 1.000 1.000 1.000
ENSG00000106829 0.684 0.443 0.531 0.701
These distances are custom measures that I need to cluster. Since it's a
symmetric matrix I only need to consider one half triangle of the matrix. So I
do something like this :-
newmat <- ensembl_copygosimmat
newmat[upper.tri(ensembl_copygosimmat)] <- NA
Then I wanted to visualize how the lower triangle looked using pheatmap which
does hierarchical clustering itself.
library(pheatmap)
pheatmap(newmat)
But since there are NA values in the matrix (in the upper half) it always
throws an error. I was wondering what would be the ideal way to visualize as
well as cluster such a matrix.
Regards
Saad
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