parse_phylowgs: parse_phylowgs Parse phylowgs outputs to visualize using...
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

Description Usage Arguments Value Examples

parse_phylowgs

Parse phylowgs outputs to visualize using EvoFreq.

1	parse_phylowgs(json_file, return_all = TRUE)

`json_file`	json file output from PhyloWGS containing tree structure and cellular prevalance information.
`return_all`	if false, return the best result based on the linearity index provided by PhyloWGS.

A list of dataframes of resolved phylogenies from PhyloWGS.

phylowgs_output="run_name.summ.json"

tree_data <- parse_phylowgs(json_file=phylowgs_output)

#EvoFreqPlots
pdf('./evofreqs.pdf', width=8, height=4, onefile = T)
for (i in 1:length(f$all)){
 clone_dynamics_df <- get_evofreq(tree_data[[i]][,c(5,length(colnames(tree_data)))], clones=tree_data[[i]]$clone, parents=tree_data[[i]]$parent, clone_cmap = "jet")
 p <- plot_evofreq(evofreq_df)
 print(p)
}
dev.off()