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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| stable = T | ||
| if (stable) { | ||
| library(RevGadgets) | ||
| } else { | ||
| source("/Users/mlandis/projects/RevGadgets/R/plot_ancestral_states.R") | ||
| } | ||
| library(ggtree) | ||
| library(ggplot2) | ||
|
|
||
| # files | ||
| tree_fn = paste(out_str, ".ase.tre", sep="") | ||
| label_fn = paste(out_str, ".state_labels.txt", sep="") | ||
| color_fn = "scripts/range_colors.txt" | ||
|
|
||
| # get state labels | ||
| state_descriptions = read.csv(label_fn, header=T, sep=",", colClasses="character") | ||
|
|
||
| # map presence-absence ranges to area names | ||
| range_labels = sapply(state_descriptions$range[2:nrow(state_descriptions)], | ||
| function(x) { | ||
| present = as.vector(gregexpr(pattern="1", x)[[1]]) | ||
| paste( area_names[present], collapse="") | ||
| }) | ||
|
|
||
| state_labels = range_labels | ||
| names(state_labels) = as.character(1:15) | ||
|
|
||
| # generate colors for ranges | ||
| range_color_list = read.csv(color_fn, header=T, sep=",", colClasses="character") | ||
| range_colors = range_color_list$color[ match(range_labels, range_color_list$range) ] | ||
|
|
||
| # plot ranges | ||
| summary_statistic = "MAPRange" | ||
| plot_ancestral_states(tree_file=tree_fn, | ||
| include_start_states=T, | ||
| shoulder_label_size=1.5, | ||
| shoulder_label_nudge_x=-0.1*plot_scale, | ||
| summary_statistic=summary_statistic, | ||
| state_labels=state_labels, | ||
| state_colors=range_colors, | ||
| node_label_size=2, | ||
| node_size_range=c(2,2), | ||
| node_label_nudge_x=0.1*plot_scale, | ||
| tip_label_size=2, | ||
| tip_label_offset=0.5*plot_scale, | ||
| xlim_visible=c(0,17*plot_scale), | ||
| show_posterior_legend=F, | ||
| show_tree_scale=T) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| stable = T | ||
| if (stable) { | ||
| library(RevGadgets) | ||
| } else { | ||
| source("/Users/mlandis/projects/RevGadgets/R/plot_ancestral_states.R") | ||
| } | ||
| library(ggtree) | ||
|
|
||
|
|
||
|
|
||
| # area labels | ||
| out_str = "output/simple" | ||
| out_str = "output/epoch" | ||
| area_names = c("K", "O", "M", "H") | ||
| s = 5/15 | ||
|
|
||
| out_str = "output/simple_phy" | ||
| area_names = c("R", "K", "O", "M", "H", "Z") | ||
| s = | ||
|
|
||
| tree_fn = paste(out_str, ".ase.tre", sep="") | ||
| label_fn = paste(out_str, ".state_labels.txt", sep="") | ||
| color_fn = "scripts/range_colors.txt" | ||
|
|
||
| # get state labels | ||
| state_descriptions = read.csv(label_fn, header=T, sep=",", colClasses="character") | ||
|
|
||
|
|
||
| # map presence-absence ranges to area names | ||
| range_labels = sapply(state_descriptions$range[2:nrow(state_descriptions)], | ||
| function(x) { | ||
| present = as.vector(gregexpr(pattern="1", x)[[1]]) | ||
| paste( area_names[present], collapse="") | ||
| }) | ||
|
|
||
| # generate colors for ranges | ||
| range_color_list = read.csv(color_fn, header=T, sep=",", colClasses="character") | ||
| range_colors = range_color_list$color[ match(range_labels, range_color_list$range) ] | ||
|
|
||
|
|
||
| # plot ranges | ||
| summary_statistic = "MAPRange" | ||
| s = 5 / 15 | ||
| plot_ancestral_states(tree_file=tree_fn, | ||
| include_start_states=T, | ||
| shoulder_label_size=1.5, | ||
| shoulder_label_nudge_x=-0.1*s, | ||
| summary_statistic=summary_statistic, | ||
| state_labels=range_labels, | ||
| state_colors=range_colors, | ||
| node_label_size=2, | ||
| node_size_range=c(2,2), | ||
| node_label_nudge_x=0.1*s, | ||
| tip_label_size=2, | ||
| tip_label_offset=s*0.5, | ||
| xlim_visible=c(0,s*17), | ||
| show_posterior_legend=F, | ||
| show_tree_scale=T) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| range,color | ||
| "K","#7570b3" | ||
| "O","#e7298a" | ||
| "M","#66a61e" | ||
| "H","#e6ab02" | ||
| "KO","orchid" | ||
| "KM","red" | ||
| "OM","green" | ||
| "KH","cyan" | ||
| "OH","cadetblue3" | ||
| "MH","tomato" |
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