maPlot(edgeR)
maPlot()所属R语言包：edgeR
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data
图数折的变化与log浓度（或M对计数数据）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
To represent counts that were low (e.g. zero in 1 library and non-zero in the other) in one of the two conditions, a 'smear' of points at low A value is presented.
代表计数低的两个条件之一，“涂抹”在点A值低（如1库和其他非零零）。
用法----------Usage----------
maPlot(x, y, logAbundance=NULL, logFC=NULL, normalize=FALSE, smearWidth = 1, col = NULL, allCol = "black", lowCol = "orange", deCol="red", de.tags=NULL, smooth.scatter=FALSE, lowess=FALSE, ...)
参数----------Arguments----------
参数：x
vector of counts or concentrations (group 1)
向量的数量或浓度组（1）
参数：y
vector of counts or concentrations (group 2)
向量的数量或浓度（第2组）
参数：logAbundance
vector providing the abundance of each tag on the log2 scale. Purely optional (default is NULL), but in combination with logFC provides a more direct way to create an MA-plot if the log-abundance and log-fold change are available.
向量提供丰富的每个标签上的log2规模。纯粹是可选的（默认是NULL），但结合logFC提供了一个更直接的方式来创建一个主图，如果log丰度和log倍。
参数：logFC
vector providing the log-fold change for each tag for a given experimental contrast. Default is NULL, only to be used together with logAbundance as both need to be non-null for their values to be used.
矢量提供的log倍的变化，为每一个给定的实验对比标签。默认值为NULL，仅可用于连同logAbundance都需要为自己的价值观非空要使用。
参数：normalize
logical, whether to divide x and y vectors by their sum
逻辑，是否划分x和y向量，其总和
参数：smearWidth
scalar, width of the smear
标量，涂抹宽度
参数：col
vector of colours for the points (if NULL, uses allCol and lowCol)
向量的点的颜色（如果NULL，使用allCol和lowCol）
参数：allCol
colour of the non-smeared points
非抹上点颜色
参数：lowCol
colour of the smeared points
抹上点颜色
参数：deCol
colour of the DE (differentially expressed) points
颜色的DE差异表达点
参数：de.tags
indices for tags identified as being differentially expressed; use exactTest to identify DE genes
指数确定为差异表达的标签，使用exactTest识别DE基因
参数：smooth.scatter
logical, whether to produce a 'smooth scatter' plot using the KernSmooth::smoothScatter function or just a regular scatter plot; default is FALSE, i.e. produce a regular scatter plot
逻辑，是否产生“顺利散射”图使用的KernSmooth :: smoothScatter功能或只是一个普通的散点图;默认为FALSE，即产生一个普通的散点图
参数：lowess
logical, indicating whether or not to add a lowess curve to the MA-plot to give an indication of any trend in the log-fold change with log-concentration
逻辑，说明是否添加一个的LOWESS曲线主图给予任何趋势在log倍log浓度变化的指示
参数：...
further arguments passed on to plot
通过进一步的论据plot
Details
详情----------Details----------
The points to be smeared are identified as being equal to the minimum in one of the two groups. The smear is created by using random uniform numbers of width smearWidth to the left of the minimum A value.
涂点被确定为等于两组最低。使用随机统一编号宽度smearWidthA值最低左涂抹创建。
值----------Value----------
a plot to the current device, and invisibly returns the M (logFC) and A (logConc) values used for the plot, plus identifiers w and v of genes for which M and A values, or just M values, respectively, were adjusted to make a nicer looking plot.
到当前设备的图，无形中返回M（logFC）A（logConc）重视图，加上标识符w和v基因MA值，或只是M值，分别进行了调整，作出更好看的图。
作者（S）----------Author(s)----------
Mark Robinson, Davis McCarthy
参见----------See Also----------
plotSmear
plotSmear
举例----------Examples----------
y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
maPlot(y[,1], y[,2])
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。
|
发表于 2012-2-25 17:08:35
