plotMA(limma)
plotMA()所属R语言包：limma
MA-Plot
MA - 图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creates an MA-plot with color coding for control spots.
创建一个主图与控制点的颜色编码。
用法----------Usage----------
plotMA(MA, array=1, xlab="A", ylab="M", main=colnames(MA)[array], xlim=NULL, ylim=NULL, status, values, pch, col, cex, legend=TRUE, zero.weights=FALSE, ...)
参数----------Arguments----------
参数：MA
an RGList, MAList or MArrayLM object, or any list with components M containing log-ratios and A containing average intensities. Alternatively a matrix or ExpressionSet object.
RGList，MAList或MArrayLM对象，或与任何组件列表M包含log比率和A包含的平均强度。另外一个matrix或ExpressionSet对象。
参数：array
integer giving the array to be plotted. Corresponds to columns of M and A.
整数，要绘制的数组。对应列M和A。
参数：xlab
character string giving label for x-axis
字符串给X轴的标签
参数：ylab
character string giving label for y-axis
为y轴的标签的字符串，
参数：main
character string giving title for plot
字符串，标题为图
参数：xlim
numeric vector of length 2 giving limits for x-axis, defaults to min and max of the data
长度为2的数字矢量最小和最大的数据为x轴，默认的限制
参数：ylim
numeric vector of length 2 giving limits for y-axis, defaults to min and max of the data
数字矢量的长度为2分钟，最大的数据为Y轴，默认的限制
参数：status
character vector giving the control status of each spot on the array, of same length as the number of rows of MA$M. If omitted, all points are plotted in the default color, symbol and size.
特征向量阵列上的每个点的控制地位，MA$M行数相同的长度。如果省略，所有点都在默认的颜色，符号和大小绘制。
参数：values
character vector giving values of status to be highlighted on the plot. Defaults to unique values of status. Ignored if there is no status vector.
status强调图给予值的特征向量。默认status唯一值。被忽略，如果有没有status向量。
参数：pch
vector or list of plotting characters. Default is integer code 16 which gives a solid circle. Ignored is there is no status vector.
向量或列表绘制字符。默认是整数代码16给出了一个实心圆。忽视的是有没有status向量。
参数：col
numeric or character vector of colors, of the same length as values. Defaults to 1:length(values). Ignored if there is no status vector.
数字或字符向量的颜色，相同长度为values。 1:length(values)默认。被忽略，如果有没有status向量。
参数：cex
numeric vector of plot symbol expansions, of the the same length as values. Defaults to 0.3 for the most common status value and 1 for the others. Ignored if there is no status vector.
数字向量积符号扩展的作为values的长度相同。 0.3默认为最常见的状态值和其他1。被忽略，如果有没有status向量。
参数：legend
logical, should a legend of plotting symbols and colors be included. Ignored if there is no status vector.
逻辑，应列入传说绘制的符号和颜色。被忽略，如果有没有status向量。
参数：zero.weights
logical, should spots with zero or negative weights be plotted?
逻辑，应绘制点与零或负重量吗？
参数：...
any other arguments are passed to plot
任何其他参数传递plot的
Details
详情----------Details----------
An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values). If MA is an RGList or MAList then this function produces an ordinary within-array MA-plot. If MA is an MArrayLM object, then the plot is an fitted model MA-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis.
一个马的图是一个log强度比（M值）与log强度的平均值（A值）的图。 MA如果RGList或MAList那么这个函数产生一个普通的阵内主图。如果MA是MArrayLM对象，然后图是拟合模型主图估计系数是x轴和y轴的平均A值。
If MA is a matrix or ExpressionSet object, then this function produces a between-array MA-plot. In this case the A-values in the plot are the average log-intensities across the arrays and the M-values are the deviations of the log-intensities for the specified array from the average. If there are more than five arays, then the average is computed robustly using medians. With five or fewer arrays, it is computed by means.
如果MA是一个matrix或ExpressionSet对象，那么这个函数产生一个阵列之间的马的图。在这种情况下，在图的A值是整个阵列log和M值平均强度从平均指定数组的log强度的偏差。如果有超过五个一阳，然后平均计算强劲使用中位数。与五个或更少的阵列，它的计算手段。
The status vector is intended to specify the control status of each spot, for example "gene", "ratio control", "house keeping gene", "buffer" and so on. The vector is usually computed using the function controlStatus and a spot-types file. However the function may be used to highlight any subset of spots.
status向量指定每个点的控制状态，例如“基因”，“比例控制”，“看家基因”，“缓冲区”等。通常的向量计算使用的功能controlStatus现货类型的文件。然而，该功能可用于突出任何点的子集。
The status can be included as the component MA$genes$Status instead of being passed as an argument to plotMA. The arguments values, pch, col and cex can be included as attributes to status instead of being passed as arguments to plotMA.
status可以作为组件MA$genes$Status而不是作为plotMA的参数通过。论据values，pch，col和cex可以作为status而不是被当作参数传递到plotMA属性。
See points for possible values for pch, col and cex.
看到pointspch，col和cex可能的值。
值----------Value----------
A plot is created on the current graphics device.
当前图形设备上创建一个图。
作者（S）----------Author(s)----------
Gordon Smyth
参考文献----------References----------
<h3>See Also</h3> An overview of diagnostic functions available in LIMMA is given in 09.Diagnostics.
举例----------Examples----------
MA <- new("MAList")
MA$A <- runif(300,4,16)
MA$M <- rt(300,df=3)
status <- rep("Gene",300)
status[1:3] <- "M=0"
MA$M[1:3] <- 0
status[4:6] <- "M=3"
MA$M[4:6] <- 3
status[7:9] <- "M=-3"
MA$M[7:9] <- -3
plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"))
# Same as above[与上述相同]
attr(status,"values") <- c("M=0","M=3","M=-3")
attr(status,"col") <- c("blue","red","green")
plotMA(MA,main="MA-Plot with Simulated Data",status=status)
# Same as above[与上述相同]
MA$genes$Status <- status
plotMA(MA,main="MA-Plot with Simulated Data")
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。
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发表于 2012-2-25 23:22:04
