plot.getLD(trio)
plot.getLD()所属R语言包：trio
Plotting a getLD or getLDlarge Object
绘制一个getLD或getLDlarge对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plots either the pairwise r^2 or D' values computed by either getLD or getLDlarge. Can also be used to plot the categorizations used in the procedure of Gabriel et al. (2002).
图无论是成对的R ^ 2或D值计算方法是getLD或getLDlarge。也可以用于绘制加布里埃尔等的过程中所使用的分类。 （2002年）。
用法----------Usage----------
## S3 method for class 'getLD'
plot(x, y = "rSquare", start = 1, end = NA, squared = TRUE,
col = NULL, xlab = "", ylab = "", cexAxis = 0.8, alpha = 0.1,
ciLD = c(0.7, 0.98), cuRecomb = 0.9, ...)
## S3 method for class 'getLDlarge'
plot(x, y = "rSquare", start = NA, end = NA, squared = TRUE,
col = NULL, xlab = "", ylab = "", cexAxis = 0.8, alpha = 0.1,
ciLD = c(0.7,0.98), cuRecomb = 0.9, ...)
参数----------Arguments----------
参数：x
the output of getLD or getLDlarge.
的输出getLD或getLDlarge。
参数：y
either "rSquare" (default), "Dprime", or "gabriel" specifying the LD values that should be plotted.
是"rSquare"（默认），"Dprime"或"gabriel"指定的LD值应该被绘制。
参数：start
integer or character string specifying the index or the name of the first SNP, respectively, that should be plotted, where the index corresponds to the column (or row if snp.in.col = FALSE) in the matrix used as input in getLD or getLDlarge.
整数或字符串如果snp.in.col = FALSE）中所使用的矩阵在getLD输入指定的索引或第一SNP的名称，分别应绘制的，在那里索引对应的列（或行或getLDlarge。
参数：end
integer or character string specifying the index or the name of the last SNP, respectively, that should be plotted.
整数或指定的索引或最后SNP的名称，分别应绘制的字符串。
参数：squared
should the r^2 values be plotted? If FALSE, the r values are plotted. Only considered if y = "rSquare".
r^2值绘制？如果FALSE，r绘制。只考虑如果y = "rSquare"。
参数：col
a vector specifying the colors used in plotting of the LD values. If y = "rSquare" or y = "Dprime", different levels of gray will be used by default (the darker, the higher is the LD value). If y = "gabriel", strong LD is by default marked by blue fields, evidence of recombination by white color, and others by yellow.
一个向量指定用于绘制的LD值的颜色。如果y = "rSquare"或y = "Dprime"，不同层次的灰色将默认使用（颜色越深，更高的是LD值）。如果y = "gabriel"，强大的LD是默认情况下，浅蓝色，白色重组的证据，和其他的黄色标记。
参数：xlab
character string naming the label of the x-axis.
字符串命名的x-轴的标签。
参数：ylab
character string naming the label of the y-axis.
字符串命名的y轴的标签。
参数：cexAxis
a numeric value specifying the relative size of the SNP names displayed at the axes of the plot.
指定一个数值的相对大小的显示的SNP名称，轴的图。
参数：alpha
numeric value between 0 and 1. Only considered if y = "gabriel". For each pair of SNPs, a two-sided 100 * (1 - alpha)% confidence interval of D' is computed, and used to specify pairs of SNPs that are either in strong LD, or show historical evidence of recombination (see ciLD and cuRecomb). All SNP pairs not falling into these two categories are specified as 'Others'.
0和1之间的数值。只考虑如果y = "gabriel"。对于每个SNP位点，对一个双面100 *（1 - alphaD）％的置信区间的计算，用于指定对单核苷酸多态性是在强烈的LD，或重组的历史证据（见ciLD和cuRecomb“）。所有SNP对不属于这两类被指定为“其他”。
参数：ciLD
numeric vector consisting of two values between 0 and 1. Only considered if y = "gabriel". If the lower bound of the confidence interval of D' for a SNP pair is larger than or equal to the first value in ciLD and the upper bound is larger than or equal to the second value, then this pair of SNP is considered to be in strong LD.
数值向量组成的两个值0和1之间。只考虑如果y = "gabriel"。如果D表示的SNP对的置信区间的下限的第一个值大于或等于ciLD和上限是大于或等于所述第二值，那么这对SNP是被认为是在强烈的LD。
参数：cuRecomb
numeric value between 0 and 1. Only considered if y = "gabriel". If the upper bound of the confidence interval of D' for a SNP pair is smaller than cuRecomb, then this pair of SNP is considered to show evidence of recombination.
0和1之间的数值。只考虑如果y = "gabriel"。如果上限的D的置信区间为SNP对小于cuRecomb，那么这对SNP被认为是证明重组。
参数：...
further arguments of image
进一步的论据image
（作者）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>
参考文献----------References----------
参见----------See Also----------
getLD, plot.LDblocks
getLD，plot.LDblocks
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 2012-10-1 12:06:04
