dotPlot(seqinr)
dotPlot()所属R语言包：seqinr
Dot Plot Comparison of two sequences
散点图两个序列的比较
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Dot plots are most likely the oldest visual representation used to compare two sequences (see Maizel and Lenk 1981 and references therein). In its simplest form, a dot is produced at position (i,j) iff character number i in the first sequence is the same as character number j in the second sequence. More eleborated forms use sliding windows and a threshold value for two windows to be considered as matched.
点图是最有可能的最古老的可视化表示，用于比较两个序列（见Maizel和伦克1981年和参考文献）。在其最简单的形式中，一个点（I，J），当且仅当字符在第一个序列号i是j的第二序列的字符数目的相同的位置处产生。更多eleborated形式使用滑动窗口，两个窗口的阈值的被视为匹配。
用法----------Usage----------
dotPlot(seq1, seq2, wsize = 1, wstep = 1, nmatch = 1, col = c("white", "black"),
xlab = deparse(substitute(seq1)), ylab = deparse(substitute(seq2)), ...)
参数----------Arguments----------
参数：seq1
the first sequence (x-axis) as a vector of single chars.
的第一序列（x-轴）作为单字符的一个向量。
参数：seq2
the second sequence (y-axis) as a vector of single char.
第二序列（y-轴）作为向量的单个字符。
参数：wsize
the size in chars of the moving window.
chars中的移动窗口的大小。
参数：wstep
the size in chars for the steps of the moving window. Use wstep == wsize for non-overlapping windows.
chars中的步骤的移动窗口的大小。使用wstep == wsize非重叠窗口。
参数：nmatch
if the number of match per window is greater than or equal to nmatch then a dot is produced.
如果如同每个窗口的数目是大于或等于nmatch然后一个点产生。
参数：col
color of points passed to image.
颜色传递给image点。
参数：xlab
label of x-axis passed to image.
标签的x轴传递给image。
参数：ylab
label of y-axis passed to image.
标签y轴传递给image。
参数：...
further arguments passed to image.
进一步的参数传递给image。
值----------Value----------
NULL.
NULL。
（作者）----------Author(s)----------
J.R. Lobry
参考文献----------References----------
Nucleic Acid and Protein Sequences. Proceedings of the National Academy of Science USA, 78:7665-7669.<br>
参见----------See Also----------
image
image
实例----------Examples----------
#[]
# Identity is on the main diagonal:[的主对角线上的身份是：]
#[]
dotPlot(letters, letters, main = "Direct repeat")
#[]
# Internal repeats are off the main diagonal:[内部重复的主对角线：]
#[]
dotPlot(rep(letters, 2), rep(letters, 2), main = "Internal repeats")
#[]
# Inversions are orthogonal to the main diagonal:[反转数是正交的主对角线：]
#[]
dotPlot(letters, rev(letters), main = "Inversion")
#[]
# Insertion in the second sequence yields a vertical jump:[在第二个序列的插入产生垂直跳跃：]
#[]
dotPlot(letters, c(letters[1:10], s2c("insertion"), letters[11:26]),
main = "Insertion in the second sequence", asp = 1)
#[]
# Insertion in the first sequence yields an horizontal jump:[第一个序列中的插入产生一个水平跳：]
#[]
dotPlot(c(letters[1:10], s2c("insertion"), letters[11:26]), letters,
main = "Insertion in the first sequence", asp = 1)
#[]
# Protein sequences have usually a good signal/noise ratio because there[蛋白质序列具有通常是一个很好的信号/噪声比，因为有]
# are 20 possible amino-acids:[有20个可能的氨基酸：]
#[]
aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
protein <- read.fasta(aafile)[[1]]
dotPlot(protein, protein, main = "Dot plot of a protein\nwsize = 1, wstep = 1, nmatch = 1")
#[]
# Nucleic acid sequences have usually a poor signal/noise ratio because[核酸序列通常具有较差的信号/噪声比，因为]
# there are only 4 different bases:[有4个不同的碱基：]
#[]
dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
dna <- protein <- read.fasta(dnafile)[[1]]
dotPlot(dna[1:200], dna[1:200], main = "Dot plot of a nucleic acid sequence\nwsize = 1, wstep = 1, nmatch = 1")
#[]
# Play with the wsize, wstep and nmatch arguments to increase the [玩的的WSIZE，wstep和nmatch参数，以增加]
# signal/noise ratio:[信号/噪声比：]
#[]
dotPlot(dna[1:200], dna[1:200], wsize = 3, wstep = 3, nmatch = 3,
main = "Dot plot of a nucleic acid sequence\nwsize = 3, wstep = 3, nmatch = 3")
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-9-30 01:16:43
