Re: [R] Visualizing and clustering one half of a symmetric matrix

2016-09-16 Thread Khan, Saad M. (MU-Student)
I do want to cluster it and only plot the lower half of the matrix. From: Peter Langfelder Sent: Thursday, September 15, 2016 11:33:13 PM To: Khan, Saad M. (MU-Student) Cc: r-help@R-project.org Subject: Re: [R] Visualizing and clustering one half of a symmetric

Re: [R] Visualizing and clustering one half of a symmetric matrix

2016-09-15 Thread Peter Langfelder
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

[R] Visualizing and clustering one half of a symmetric matrix

2016-09-15 Thread Khan, Saad M. (MU-Student)
Hi all, I have a distance matrix (symmetric) which looks somewhat like this (only a small portion shown) ENSG0101413 ENSG0176884 ENSG0185532 ENSG0106829 ENSG0101413 1.000 1.000 1.000 1.000 ENSG0176884 0.328