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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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Some genomes not displaying on tree #146

Closed tbazilegith closed 1 year ago

tbazilegith commented 1 year ago

Hi Xavier, After running the script cfml_results.R, I noticed that some genomes do not display on tree while their branches seem to be there. I saw on previous post that the warning wouldn't a problem, but wonder why only certain genomes display. For I have 86 genomes. Any ideas about that? Warning message: In ifelse(is.na(as.numeric(rownames(wh.mut))), rownames(wh.mut), : NAs introduced by coercion null device 1 [[1]] NULL

[[2]] NULL ... [[84]] NULL

[[85]] NULL

null device 1

Thanks, TJ

xavierdidelot commented 1 year ago

Sometimes labels are not shown if they are too long, so that there is no space for them. You will have to edit the script to solve this or add the labels separately.

tbazilegith commented 1 year ago

Thanks! I work on that. Also, when I notice recombination on a branch such as long dark blue line, how do I correct that? Thanks again

xavierdidelot commented 1 year ago

This is already corrected in the ClonalFrameML output tree.

tbazilegith commented 1 year ago

Perfect! So that means the tree topology reflects the correction?

xavierdidelot commented 1 year ago

The branch lengths are corrected. ClonalFrameML does not change the tree topology.

tbazilegith commented 1 year ago

Thanks!