[R] Visualizing and clustering one half of a symmetric matrix
Peter Langfelder
peter.langfelder at gmail.com
Fri Sep 16 06:33:13 CEST 2016
Do not set the upper (or lower) triangle to NA. Simply supply the full
matrix to pheatmap. I am not an expert on pheatmap but looking at the
manual you should supply clustering_distance_rows = "none",
clustering_distance_cols = "none" or something like that to make
pheatmap interpret the matrix as a distance matrix. Read carefully
through the help on pheatmap to make sure the function plots what you
want it to plot.
HTH,
Peter
On Thu, Sep 15, 2016 at 7:38 PM, Khan, Saad M. (MU-Student)
<smk5g5 at mail.missouri.edu> wrote:
> 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
>
> [[alternative HTML version deleted]]
>
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