plotMDS.DGEList(edgeR)
plotMDS.DGEList()所属R语言包：edgeR
Multidimensional scaling plot of digital gene expression profiles
数字基因表达谱的多维尺度图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculate distances between RNA-seq or DGE libraries, then produce a multidimensional scaling plot. Distances on the plot represent coefficient of variation of expression between samples for the top genes that best distinguish the samples.
计算RNA-seq的或DGE库之间的距离，然后产生多维缩放图。图上的距离代表表达之间的顶端，最好的区分样品的基因样本的变异系数。
用法----------Usage----------
## S3 method for class 'DGEList'
plotMDS(x, top=500, labels=colnames(x), col=NULL, cex=1, dim.plot=c(1, 2), ndim=max(dim.plot), xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]), ...)
参数----------Arguments----------
参数：x
any matrix or DGEList object.
任何矩阵或DGEList对象。
参数：top
number of top genes used to calculate pairwise distances.
顶级基因的数量来计算成对距离。
参数：labels
character vector of sample names or labels. If x has no column names, then defaults the index of the samples.
样品名称或标签的特征向量。 x如果有没有列名，则默认的指数样本。
参数：col
numeric or character vector of colors for the plotting characters. See text for possible values.
数字或字符的矢量绘图字符的颜色。看到text可能的值。
参数：cex
numeric vector of plot symbol expansions. See text for possible values.
数字向量积符号扩展。看到text可能的值。
参数：dim.plot
which two dimensions should be plotted, numeric vector of length two.
这两个方面，应绘制，长度为二的数字向量。
参数：ndim
number of dimensions in which data is to be represented
维数中的数据是代表
参数：xlab
title for the x-axis
x轴标题
参数：ylab
title for the y-axis
y轴标题
参数：...
any other arguments are passed to plot.
任何其他的参数被传递到plot。
Details
详情----------Details----------
This function is a variation on the usual multdimensional scaling (or principle coordinate) plot, in that a distance measure particularly appropriate for the digital gene expression (DGE) context is used. A set of top genes are chosen that have largest biological variation between the libraries (those with largest tagwise dispersion treating all libraries as one group). Then the distance between each pair of libraries (columns) is the biological coefficient of variation (square root of the common dispersion) between those two libraries alone, using the top genes.
此功能上通常multdimensional缩放（或原则坐标）的图，在这个距离的措施，特别是适当的数字基因表达（DGE）上下文的变化。选择一套顶级基因库（那些最大的tagwise分散当作一组的所有库）之间最大的生物变异。然后，每库（列）之间的距离是生物的变异系数（常见的色散平方根），仅这两个库之间使用顶部的基因。
The number top of top genes chosen for this exercise should roughly correspond to the number of differentially expressed genes with materially large fold-changes. The default setting of 500 genes is widely effective and suitable for routine use, but a smaller value might be chosen for when the samples are distinguished by a specific focused molecular pathway. Very large values (greater than 1000) are not usually so effective.
数量top这次演习选择的顶级基因应该大致符合重大大的fold change的差异表达基因的数目。默认设置的500个基因是广泛有效的，适合日常使用，但可能选择较小的值时，样品集中由一个特定的分子途径来区分。非常大的数值（大于1000）通常不那么有效。
This function can be slow when there are many libraries.
此功能可能会很慢时，有许多图书馆。
值----------Value----------
A plot is created on the current graphics device.
当前图形设备上创建一个图。
An object of class "MDS" is invisibly returned. This is a list containing the following components:
"MDS"类的对象是无形返回。这是一个列表，其中包含以下组件：
参数：distance.matrix
numeric matrix of pairwise distances between columns of x
数字矩阵成对x列之间的距离
参数：cmdscale.out
output from the function cmdscale given the distance matrix
输出功能cmdscale给定的距离矩阵
参数：dim.plot
dimensions plotted
尺寸绘制
参数：x
x-xordinates of plotted points
X-xordinates绘制点
参数：y
y-cordinates of plotted points
Y-cordinates绘制点
作者（S）----------Author(s)----------
Yunshun Chen and Gordon Smyth
参见----------See Also----------
cmdscale, as.dist, plotMDS
cmdscale，as.dist，plotMDS
举例----------Examples----------
# Simulate DGE data for 1000 genes(tags) and 6 samples.[模拟胃排空1000个基因（标签）和6个样品的数据。]
# Samples are in two groups[样品是在两组]
# First 300 genes are differentially expressed in second group[在第二组第300基因的差异表达]
y <- matrix(rnbinom(6000, size = 1/2, mu = 10),1000,6)
rownames(y) <- paste("Gene",1:1000)
y[1:300,4:6] <- y[1:300,4:6] + 10
# without labels, indexes of samples are plotted.[无标签样本的指标绘制。]
mds <- plotMDS(y, col=c(rep("black",3), rep("red",3)) )
# or labels can be provided, here group indicators:[或标签可提供组指标：]
plotMDS(mds, col=c(rep("black",3), rep("red",3)), labels= c(rep("Grp1",3), rep("Grp2",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 2012-2-25 17:09:27
