提取OTU表格中分类学名称
在分类学注释结果中，物种的分类学名称包含所有的分类学水平，在绘制相对丰度图或绘制热图时，需要对分类学名称进行处理，只保留我们需要的分类学水平。
这里以L4水平为例，用到的函数为gsub函数（http://www.endmemo.com/r/gsub.php）
gsub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)
• pattern: string to be matched, supports regular expression
• replacement: string for replacement
• x: string or string vector
• perl: logical. Should perl-compatible regexps be used? Has priority over extended
• fixed: logical. If TRUE, pattern is a string to be matched as is. Overrides all conflicting arguments
• useBytes: logical. If TRUE the matching is done byte-by-byte rather than character-by-character
gsub()可以用于字段的删减、增补、替换和切割，可以处理一个字段也可以处理由字段组成的向量。
具体的使用方法为：gsub("目标字符", "替换字符", 对象)
在gsub函数中，任何字段处理都由将“替换字符”替换到“目标字符”这一流程中实现，令替换字符为''''可实现删除，令替换字符为"目标字符+增补内容"可实现增补，替换和切也是使用类似的操作。
Regular Expression Syntax:
Syntax
Description
\\d Digit, 0,1,2 ... 9
\\D Not Digit
\\s Space
\\S Not Space
\\w Word
\\W Not Word
\\t Tab
\\n New line
^ Beginning of the string
$ End of the string
\ Escape special characters, e.g. \\ is "\", \+ is "+"
| Alternation match. e.g. /(e|d)n/ matches "en" and "dn"
• Any character, except \n or line terminator
[ab] a or b
[^ab] Any character except a and b
[0-9] All Digit
[A-Z] All uppercase A to Z letters
[a-z] All lowercase a to z letters
[A-z] All Uppercase and lowercase a to z letters
i+ i at least one time
i* i zero or more times
i? i zero or 1 time
i{n} i occurs n times in sequence
i{n1,n2} i occurs n1 - n2 times in sequence
i{n1,n2}? non greedy match, see above example
i{n,} i occures >= n times
[:alnum:] Alphanumeric characters: [:alpha:] and [:digit:]
[:alpha:] Alphabetic characters: [:lower:] and [:upper:]
[:blank:] Blank characters: e.g. space, tab
[:cntrl:] Control characters
[:digit:] Digits: 0 1 2 3 4 5 6 7 8 9
[:graph:] Graphical characters: [:alnum:] and [:punct:]
[:lower:] Lower-case letters in the current locale
[:print:] Printable characters: [:alnum:], [:punct:] and space
[:punct:] Punctuation character: ! " # $ % & ' ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ ` { | } ~
[:space:] Space characters: tab, newline, vertical tab, form feed, carriage return, space
[:upper:] Upper-case letters in the current locale
[:xdigit:] Hexadecimal digits: 0 1 2 3 4 5 6 7 8 9 A B C D E F a b c d e f
示例
abundance <- read.table("otu_taxa_table_L4.txt",header = TRUE,sep = "\t")
abundance <- as.data.frame(abundance)
taxon <- gsub(".*(o__)","",abundance$Taxon)
taxon <- gsub(".*(;)","",taxon)
taxon <- gsub(".*(Other)","",taxon)
taxon <- gsub("(\\[)","",taxon)
taxon <- gsub("(\\])","",taxon)
abundance$Taxon <- taxon
abundance[abundance==""] <- NA
abundance <- na.omit(abundance)
abundance <- subset(abundance,Taxon != "Unclassified")
abundance <- subset(abundance,Taxon != "norank")
abundance <- subset(abundance,Taxon != "uncultured")
abundance <- t(abundance)
colnames(abundance) <- abundance[1,]
abundance <- abundance[-1,]