Chris Miller
Chris Miller
One option would be to add an additional, unlabeled timepoint just to the right of your DX, and have your yellow clone start there.
Your assignments don't really make sense there. For example, you have cluster 2 (39.4/28.3) being a parent of itself. If it's derived from one of the other clusters, that cluster...
Right, that's not a configurable option at present. Happy to accept pull requests if you'd like to hack that feature in!
fantastic! happy to look it over if you make a PR
Closed in https://github.com/chrisamiller/fishplot/pull/26 Thanks again for the contribution!
You're going to have to provide more information, including the exact parameters and command that you ran the tool with.
I'll add it to my list - PRs welcome! ;)
``` ##convert means back out of log space into absolute copy number segs$seg.mean=(2^segs$seg.mean)*2 ``` to convert from log2 copy number to absolute (2 = cn neutral, 1 = loss, etc),...
1) the output is expressed in terms of copy number, where 2 equals CN neutral. There may be many factors that cause the CN to be something other than integer...
Does your VCF contain the DP and AF1 fields in your info column? Can you paste a few lines from your VCF file for troubleshooting?