Khan, Saad M. (MU-Student)
2016-Sep-16 02:38 UTC
[R] Visualizing and clustering one half of a symmetric matrix
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]]
Peter Langfelder
2016-Sep-16 04:33 UTC
[R] Visualizing and clustering one half of a symmetric matrix
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]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Khan, Saad M. (MU-Student)
2016-Sep-16 04:40 UTC
[R] Visualizing and clustering one half of a symmetric matrix
I do want to cluster it and only plot the lower half of the matrix. ________________________________ From: Peter Langfelder <peter.langfelder at gmail.com> Sent: Thursday, September 15, 2016 11:33:13 PM To: Khan, Saad M. (MU-Student) Cc: r-help at R-project.org Subject: Re: [R] Visualizing and clustering one half of a symmetric matrix 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]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.[[alternative HTML version deleted]]