iTOL辅助R包itol.toolkit学习笔记

写在前面

还是学学这个点点鼠标就能搞定的神器iTOL。。。PS：其实暑假是闲着没事干了，数据在服务器跑着要一个月。

安装

直接从GitHub安装最新版：

devtools::install_github("TongZhou2017/itol.toolkit")

快速开始

library(itol.toolkit)

# read data
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
data("template_groups")
df_group <- data.frame(id = unique(template_groups$group), 
                       data = unique(template_groups$group))

# create hub
hub <- create_hub(tree = tree)

## create unit
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "DATASET_COLORSTRIP", 
                    tree = tree)

## add unit into hub
hub <- hub + unit

## write template file
write_hub(hub,getwd())

折叠分支

有两种方法可以选择：

• 根据分支名称进行折叠；
• 根据Node ID进行折叠。

个人更倾向于第二种方法：

使用iTOL就可以显示Node ID:

现在我准备折叠I15和text这两个分支：

# 折叠分支
library(itol.toolkit)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
data("template_groups")
group_names <- unique(c("I15", "text"))
unit_2 <- create_unit(data = group_names, 
                      key = "E002_collapse_2", 
                      type = "COLLAPSE", 
                      tree = tree)
write_unit(unit_2,
           paste0(getwd(),"/E002_collapse_2.txt"))

标签的背景色

# 标签的背景色
library(itol.toolkit)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
hub <- create_hub(tree = tree)
data("template_groups")

unit_7 <- create_unit(data = template_groups, 
                      key = "E007_tree_colors_1", 
                      type = "TREE_COLORS", 
                      subtype = "range", 
                      tree = tree)
write_unit(unit_7)

可以自行调节：

简单柱状图

# 添加柱状图
library(itol.toolkit)
library(data.table)
library(tidyr)
library(dplyr)
library(stringr)
library(ape)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
df_frequence <- system.file("extdata",
                            "templates_frequence.txt",
                            package = "itol.toolkit")
df_frequence <- fread(df_frequence)
names(df_frequence) <- c(
  "id",
  "Li,S. et al. (2022) J. Hazard. Mater.","Zheng,L. et al. (2022) Environ. Pollut.",
  "Welter,D.K. et al. (2021) mSystems",
  "Zhang,L et al. (2022) Nat. Commun.",
  "Rubbens,P. et al. (2019) mSystems",
  "Laidoudi,Y. et al. (2022) Pathogens",
  "Wang,Y. et al. (2022) Nat. Commun.",
  "Ceres,K.M. et al. (2022) Microb. Genomics",
  "Youngblut,N.D. et al. (2019) Nat. Commun.",
  "Balvín,O. et al. (2018) Sci. Rep.",
  "Prostak,S.M. et al. (2021) Curr. Biol.",
  "Dijkhuizen,L.W. et al. (2021) Front. Plant Sci.",
  "Zhang,X. et al. (2022) Microbiol. Spectr.",
  "Peris,D. et al. (2022) PLOS Genet.",
  "Denamur,E. et al. (2022) PLOS Genet.",
  "Dezordi,F.Z. et al. (2022) bioRxiv",
  "Lin,Y. et al. (2021) Microbiome",
  "Wang,Y. et al. (2022) bioRxiv",
  "Qi,Z. et al. (2022) Food Control",
  "Zhou,X. et al. (2022) Food Res. Int.",
  "Zhou,X. et al. (2022) Nat. Commun.")
names(df_frequence) <- stringr::str_remove_all(names(df_frequence),"[()]")
names(df_frequence) <- stringr::str_replace_all(names(df_frequence),",","-")

unit_29 <- create_unit(data = df_frequence,
                       key = "E029_simplebar_1",
                       type = "DATASET_SIMPLEBAR",
                       tree = tree)
write_unit(unit_29)

unit_30 <- create_unit(data = df_frequence,
                       key = "E030_simplebar_2",
                       type = "DATASET_SIMPLEBAR",
                       method = "mean",
                       tree = tree)
write_unit(unit_30)

添加热图

# 添加热图
library(itol.toolkit)
library(data.table)
library(ape)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
df_frequence <- system.file("extdata",
                            "templates_frequence.txt",
                            package = "itol.toolkit")
df_frequence <- fread(df_frequence)

unit_25 <- create_unit(data = df_frequence,
                       key = "E025_heatmap_1",
                       type = "DATASET_HEATMAP",
                       tree = tree)
unit_25@specific_themes$heatmap$color$min <- "#ffd966"
unit_25@specific_themes$heatmap$color$max <- "#cc0000"
unit_25@specific_themes$heatmap$use_mid <- 0
write_unit(unit_25)

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基本的思路搞定了，先实战一下再说。