set.seed(1234)
tree <- rtree(n = 7, rooted = TRUE)
tree$node.label <- paste0("n", Ntip(tree) + 1:Nnode(tree))
plot(tree)
## Numeric
states <- c(t1 = 37, t2 = NA, t3 = NA, t4 = NA, t5 = 10, t6 = 80, t7 = NA)
states <- states[match(tree$tip.label, names(states))]
tip_data_1 <- data.frame(
label = tree$tip.label,
value = states,
color = "annotated tip"
)
p <- ggtree(tree) %<+% tip_data_1
p +
geom_tiplab() +
geom_nodelab(nudge_x = -0.07, nudge_y = 0.15) +
geom_label(aes(label = value, fill = color), nudge_x = 0.11, na.rm = TRUE, alpha = 0.5) +
scale_fill_manual(values = "red", breaks = "annotated tip")
pruned_states <- states[!is.na(states)]
pruned_tree <- keep.tip(tree, tip = names(pruned_states))
pruned_tip_data <- data.frame(
label = names(pruned_states),
value = pruned_states,
color = "annotated tip"
)
pruned_asr <- asr_squared_change_parsimony(
tree = pruned_tree, tip_states = pruned_states, check_input = FALSE
)$ancestral_states
pruned_node_data <- data.frame(
label = tree$node.label,
value = round(pruned_asr),
color = "ASR node"
)
pruned_tree_data <- rbind(pruned_tip_data, pruned_node_data)
pruned_p <- ggtree(pruned_tree) %<+% pruned_tree_data
pruned_p +
geom_tiplab() +
geom_nodelab(nudge_x = -0.07, nudge_y = 0.15) +
geom_label(aes(label = value, fill = color), nudge_x = 0.11, na.rm = TRUE, alpha = 0.5) +
scale_fill_manual(
values = c("red", "blue"), breaks = c("annotated tip", "ASR node")
)
res <- hsp_squared_change_parsimony(
tree = tree, tip_states = states, check_input = FALSE, weighted = TRUE
)
pred <- res$states
names(pred) <- c(tree$tip.label, tree$node.label)
pred_tree_data <- data.frame(
label = names(pred),
value = floor(pred)
) |>
mutate(
color = case_when(
label %in% names(states[!is.na(states)]) ~ "annotated tip",
label %in% pruned_tree$node.label ~ "ASR node",
TRUE ~ "predicted tip/node"
)
)
p <- ggtree(tree) %<+% pred_tree_data
p +
geom_tiplab() +
geom_nodelab(nudge_x = -0.07, nudge_y = 0.15) +
geom_label(aes(label = value, fill = color), nudge_x = 0.12, alpha = 0.5) +
scale_fill_manual(
values = c("red", "blue", "yellow"), breaks = c("annotated tip", "ASR node", "predicted tip/node")
)
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> os Ubuntu 22.04.4 LTS
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#> ui X11
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#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2024-07-23
#> pandoc 3.2 @ /usr/bin/ (via rmarkdown)
#>
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#> ──────────────────────────────────────────────────────────────────────────────