treeview: Generate interactive tree visualisations and scatter plots...

In oliviabboyd/tfpscanner_preview: Transmission fitness polymorphism scanner

Generate interactive tree visualisations and scatter plots for illustrating scannint statistics.

Description

This will produce a set of html widgets which will highlight by colour and tooltips statistics such as growth rate and molecular clock outliers.

Usage

treeview(
  e0,
  branch_cols = c("logistic_growth_rate", "clock_outlier"),
  mutations = c("S:A222V", "S:Y145H", "N:Q9L", "S:E484K"),
  lineages = c("AY\\.9", "AY\\.43", "AY\\.4\\.2"),
  output_dir = "treeview"
)

Arguments

e0	Path to the scanner environment produced by tfpscan. Alternatively can pass the environment directly.
branch_cols	A character vector of statistics for which outputs should be produced. The logistic growth rate plot will always be produced.
mutations	A character vector of mutations which will be illustrated in a heatmap
lineages	A set of lineage names which will be used to subdivide outputs in scatter plots.
output_dir	Outputs will be saved in this directory. Will create the directory if it does not exist.
pldf	the data element of a tree plot

Value

A ggtree plot

oliviabboyd/tfpscanner_preview documentation built on Dec. 4, 2022, 4:20 a.m.