Question: Question regarding sample size in SNPRelate Package in R
gravatar for ayang
4.0 years ago by
United States
ayang0 wrote:


I am trying to construct a phylogenetic tree using SNP data from a group of 9 samples. I am trying to do this using SNPRelate, but after doing the following steps below, I am encountering what seems like a simple issue that I can not seem to figure out.

The steps I conducted to get the phylogenetic tree:

(1) snpgdsDiss 
(2) snpgdsHCluster
(3) snpgdsCutTree
(4) snpgdsDrawTree

The issue I am encountering:

I have a phylogenetic tree for samples 1, 2, 3, 4, 5, 6, 7, 8, and 9 and should be able to differentiate the group based on the plot character's color. However, no matter what I do, I can't seem to use more than 8 colors. So I am having trouble differentiating the location between sample 2 and sample 5; both their plot character's color is black. Whereas, I am able to differentiate the location between the other samples, because they are red, green, dark blue, light blue, pink, yellow, and grey. 

Has anyone encounter this problem when using snpgdsDrawTree function?


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