Are there any detailed description of the output pdf from cfml_results.R?

xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

GNU General Public License v3.0

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Are there any detailed description of the output pdf from cfml_results.R? #137

Closed 1996xjm closed 1 year ago

1996xjm commented 1 year ago

I want to know what different colors of vertical bars represent?

"skyblue"
"white"
"yellow"
"orange"
"red"

@tseemann @xavierdidelot

xavierdidelot commented 1 year ago

The dark blue horizontal bars represent recombination. If a site does not change on a given branch, it is shown in light blue. If a site changes on a given branch, it is shown in a color indicating its level of homoplasy: white is no homoplasy and the range from yellow to orange to red is increasing degrees of homoplasy.