Requires the reticulate package and an installation of python (the lineage definitions are stored in a python file, and I’m not a good enough programmer to parse it).
plot_lineage_defs2() can handle cases where mutations/lineages are completely missing from one of the defs.
pkgdown() site complete.
Version 0.5.4: What will I do with all these lineage definitions?
Visualize which mutations were used the most with plot_actual_defs(res, type = "used")!
Visualize the coverage for each mutation used with plot_actual_defs(res, type = "coverage")!
Colours are always going to be a pain, but plot_lineage_defs2() has been overhauled to be a little easier.
Bugfixes:
error in plot and autoplot when by_col was NULL.
Version 0.5.3: What does that lineage definition look like to you?
Added a plotting function plot_lineage_defs() for a single lineage definition matrix. Made it pretty.
Added a plotting function plot_lineage_defs2() that compares two lineage definition matrices. Made it pretty.
Allows for user-specified colours, which was hard and probably won’t be used much but I’m happy with it.
Accepts output of provoc(), from which it will extract the actual lineage defintions used.
Version 0.5.2: Call it what you want.
Documentation has been significantly updated.
BREAKING CHANGE: If you use the argument by = "sra", the result will have a column labelled sra (not group, as before).
Version 0.5.1: “Lineages of Concern” doesn’t have the same ring to it.
BREAKING CHANGE: All names changed from “variant” to “lineage” (except in “variant of concern”).
varmat has been changed to lineage_defs because that’s much clearer.
Minor documentation updates, mainly failed inheritance.