inst/docs/cn/cookbook.md

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

示例集锦

常见任务的即拷即用配方。所有示例均使用内置的 example_tree。

以不同于折叠的阶元着色

p <- plot_timetree(example_tree, rank = "phylum",
                   color_rank = "class", unit = "Ma")

高亮特殊祖先节点

p <- plot_timetree(example_tree, rank = "phylum",
                   highlight = "LUCA", unit = "Ma")

使用精确的自定义颜色

p <- plot_timetree(example_tree, rank = "phylum",
                   color_mapping = c("Firmicutes" = "#E41A1C",
                                     "Proteobacteria" = "#377EB8"),
                   unit = "Ma")

图例置于顶部并分两列

p <- plot_timetree(example_tree, rank = "phylum",
                   legend_position = "top", legend_ncol = 2, unit = "Ma")

大树隐藏末端标签

p <- plot_timetree(example_tree, rank = "phylum",
                   show_tip_label = FALSE, unit = "Ma")

按 cladogram 绘制（忽略枝长）

p <- plot_timetree(example_tree, rank = "phylum",
                   ignore_branch_length = TRUE, unit = "Ma")

绘图前检测标签格式

labels <- example_tree$tip.label
detect_taxonomy_format(labels)

交叉校验树与序列文件

validate_tree_sequence_match(example_tree, "seqs.fasta", mol_type = "DNA")

检查分组的单系性

check_monophyly(example_tree, group = "Firmicutes", rank = "phylum")

为自己的分组生成调色板

groups <- c("Firmicutes", "Proteobacteria", "Bacteroidetes")
generate_colors(groups, palette = "viridis")

为某次运行开启详细日志

set_log_level("DEBUG")
set_log_file("rclade_run.log")
p <- plot_timetree(example_tree, rank = "phylum", unit = "Ma")

为流程阶段计时

timer_start("collapse")
p <- plot_timetree(example_tree, rank = "phylum", unit = "Ma")
timer_stop("collapse")

保存可复现的会话记录

save_session_info("session_info.txt")

另见参考手册索引。

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.