table2itol怎么安装设置

本篇内容介绍了"table2itol怎么安装设置"的有关知识，在实际案例的操作过程中，不少人都会遇到这样的困境，接下来就让小编带领大家学习一下如何处理这些情况吧！希望大家仔细阅读，能够学有所成！

table2itol简介

table2itol是在GitHup上公开的R语言包，其作用是专门为iTOL生成所需的注释文件，只需准备表格形式的数据，包含配色方案的注释文件就会自动生成，极大提高了准备注释文件的效率。

table2itol下载安装

对于习惯使用Linux系统的同学，可以这样安装：

wget https://github.com/mgoeker/table2itol/archive/master.zip unzip master.zip ## 测试 cd table2itol-masterRscript table2itol.R  chmod +x table2itol.R  ./table2itol.R

习惯使用Windows系统的同学，可以这样安装：

GitHup上直接下载table2itol压缩包，解压后放在 F:\software 文件夹下。在R或Rstudio中导入table2itol.R。

setwd("F:/software/table2itol-master")source("table2itol.R")

table2itol依赖包安装

在R或Rstudio中，安装方法如下：

### 安装依赖包 site="https://mirrors.tuna.tsinghua.edu.cn/CRAN" # 依赖包列表：参数解析、数据变换、绘图和开发包安装、安装依赖、ggplot主题 package_list = c("grid","ggplot2","gridExtra","vegan","reshape2","readODS") # 判断R包加载是否成功来决定是否安装后再加载 for(p in package_list){      if(!suppressWarnings(suppressMessages(require(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)))){           install.packages(p, repos=site)           suppressWarnings(suppressMessages(library(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)))       } }  #### 安装缺少的R包 source("http://bioconductor.org/biocLite.R") biocLite(c("optparse", "plotrix", "readODS", "readxl", "yaml"))

输入文件准备

table2itol的输入文件格式很多，以最常用的表格为例

选项设置

table2itol.R的选项有很多，不同选项可生成不同的注释文件，选项列表如下：

Options:        -a, --abort                Abort if a requested column cannot be found instead of just skipping the data set [default: FALSE]        -b NAME, --background=NAME                Column to define the background colours of the tip labels; empty means no background colours [default: ]        -c NAME, --conversion=NAME                Convert integer columns to factors ('factor') or numbers with decimal points ('double') or just not 0/1 to logical vectors ('keep') [default: none]        -C FILE, --colour-file=FILE                File in YAML format defining alternative colour vectors for domain output [default: ]        -d, --double-to-bars                Create bar charts, not gradients, from numbers with decimal points ('double') [default: FALSE]        -D DIR, --directory=DIR                Place output files in this directory ('.' means working directory, empty means input file directory) [default: .]        -e NAME, --emblems=NAME                Column to define symbol assignments; ignored if empty [default: ]        -f NUMBER, --favour=NUMBER                Numeric factor for favouring colours over symbols (higher => more colours relative to symbols) [default: 1]        -G FILE, --gradient-file=FILE                File in YAML format defining alternative colours for gradient and binary output [default: ]        -h, --help                Show this help message, then exit [default: FALSE]        -i NAME, --identifier=NAME                Mandatory identifier column; after modification as defined by --template this column must yield the tip labels of the tree [default: ID]        -j NAME, --identifier2=NAME                Optional 2nd identifier column, causing output of branchsymbols; together with -i this identifies a node [default: ]        -l NAME, --label=NAME                Column to define the tip labels displayed in the picture in place of the tip labels found in the tree [default: Label]        -m INTEGER, --max-size=INTEGER                Exceeding this threshold causes fewer colours and more symbols to be selected (see also --favour); also determines size of branch symbols [default: 20]        -n TEXT, --na-strings=TEXT                Sentinels for missing input values; several can be provided, separated by the value of --separator [default:    (null)  NA]        -o NUMBER, --opacity=NUMBER                Numeric factor for the transparency of the colours (0 => transparent, 1 => fully opaque) [default: 1]        -p INTEGER, --precision=INTEGER                Number of decimal points used in the gradient legends [default: 1]        -r TEXT/NUMBER, --restrict=TEXT/NUMBER                How to select from numeric values that yield branch symbols [default: ]        -s CHARACTER, --separator=CHARACTER                Input column separator for CSV-like files [default:     ]        -t PATTERN, --template=PATTERN                Template for sprintf function to convert ID column when deviating from tip labels [default: %s]        -w NUMBER, --width=NUMBER                Border with used for domains, colour strips etc. [default: 0.5]

也可在解压安装目录下的 table2itol_help.txt 文件或者直接调用帮助信息查看。大家灵活选择使用的选项即可。

生成注释文件

文件准备完成后就需要生成注释文件了，有两种方式生成：一种为linux下命令行运行方式，另一种是在R或Rstudio中运行。

linux下命令行运行：

./table2itol.R --na-strings X --identifier Tip --label Name ann1.tsv ann2.tsv

R或Rstudio中运行：

source("table2itol.R") create_itol_files(infiles = c("ann1.tsv", "ann2.tsv"),   identifier = "Tip", label = "Name", na.strings = "X")

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