plotDensities(limma)
plotDensities()所属R语言包：limma
Individual-channel Densities Plot
个别的通道密度图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plots the densities of individual-channel intensities for two-color microarray data.
两色的微阵列数据的个别通道的强度，密度的图。
用法----------Usage----------
plotDensities(object, log=TRUE, arrays=NULL, singlechannels=NULL, groups=NULL, col=NULL)
参数----------Arguments----------
参数：object
an RGList or MAList object. RGList objects containing logged or unlogged intensities can be accommodated using the log.transform argument.
RGList或MAList对象。 RGList对象包含记录，或者未记录的强度，可容纳使用log.transform参数。
参数：log
logical, should densities be formed and plotted for the log-intensities (TRUE) or raw intensities (FALSE)?
逻辑，应该密度形成和绘制的log，强度（TRUE）或原始强度（FALSE）？
参数：arrays
vector of integers giving the arrays from which the individual-channels will be selected to be plotted. Corresponds to columns of M and A (or R and G). Defaults to all arrays.
给阵列，从各个渠道将被选中要绘制的整数向量。对应M和A（或R和G）列。默认所有阵列。
参数：singlechannels
vector of integers indicating which individual-channels will be selected to be plotted. Values correspond to the columns of the matrix of cbind(R,G) and range between 1:ncol(R) for red channels and ( (ncol(R)+1) ncol(R)+ncol(G)) ) for the green channels in object. Defaults to all channels.
个别通道将被选中要绘制的整数向量。值对应到矩阵列cbind(R,G)与范围1:ncol(R)红色通道和( (ncol(R)+1)ncol(R)+ncol(G)) )object绿色通道。默认所有通道。
参数：groups
vector of consecutive integers beginning at 1 indicating the groups of arrays or individual-channels (depending on which of arrays or singlechannels are non NULL). This is used to color any groups of the individual-channel densities. If NULL (default), groups correspond to the red and green channels. If both arrays and singlechannels are NULL all arrays are selected and groups (if specified) must correspond to the arrays.
从1开始的连续整数的向量表示阵列或个别通道组（取决于arrays或singlechannels非NULL）。这是用来上色任何团体的个别通道密度。如果NULL（默认），groups对应的红色和绿色通道。如果双方arrays和singlechannels是NULL所有阵列选择和组（如果指定）必须符合阵列。
参数：col
vector of colors of the same length as the number of different groups. If NULL (default) the col equals c("red","green"). See details for more specifications.
颜色为不同群体的数量相同长度的向量。如果NULL（默认）col等于c("red","green")的。看到更多的规格细节。
Details
详情----------Details----------
This function is used as a data display technique associated with between-array normalization, especially individual-channel normalization methods such as quantile-normalization. See the section on between-array normalization in the LIMMA User's Guide.
这个函数是用来作为数据显示与阵列之间的标准化，特别是个别通道归一化方法，如位数标准化相关的技术。看到阵列之间的标准化在该LIMMA用户指南。
If no col is specified, the default is to color individual channels according to red and green. If both arrays and groups are non-NULL, then the length of groups must equal the length of arrays and the maximum of groups (i.e. the number of groups) must equal the length of col otherwise the default color of black will be used for all individual-channels. If arrays is NULL and both singlechannels and groups are non-NULL, then the length of groups must equal the length of singlechannels and the maximum of groups (i.e. the number of groups) must equal the length of col otherwise the default color of black will be used for all individual-channels.
如果没有col指定，默认是根据红色和绿色色独立渠道。如果这两个arrays和groups非NULL，则groups长度必须等于arrays的长度和groups最大的 （即组数）必须等于col否则默认颜色黑将所有个人渠道的长度。如果arrays是NULL都singlechannels和groups都是非NULL，然后的groups长度必须等于长度singlechannels和最大groups（即组数）必须等于长度col否则默认颜色黑将所有个人渠道。
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)----------
Natalie Thorne
参见----------See Also----------
An overview of diagnostic plots in LIMMA is given in 09.Diagnostics. There is a section using plotDensities in conjunction with between-array normalization in the LIMMA User's Guide.
在LIMMA诊断图概述在09.Diagnostics。使用配合阵列之间的LIMMA用户指南标准化plotDensities有一节。
举例----------Examples----------
## Not run: [＃无法运行：]
# This example is designed for work on a subset of the data[这个范例是专为数据的一个子集的工作]
# from the ApoAI case study in Limma User's Guide[载脂蛋白AI在Limma用户指南案例研究]
# This example was formerly loaded from sma package using[这个例子是以前从SMA使用包装]
# library(sma)[库（SMA）]
# data(MouseArray)[数据（MouseArray）]
# no normalization but background correction is done[没有标准化，但背景校正完成]
MA.n <- MA.RG(mouse.data)
# Default settings for plotDensities.[设置默认plotDensities。]
plotDensities(MA.n)
# One can reproduce the default settings.[一个可以复制的默认设置。]
plotDensities(MA.n,arrays=c(1:6),groups=c(rep(1,6),rep(2,6)),
col=c("red","green"))
# Color R and G individual-channels by blue and purple.[蓝色和紫色的颜色R和G个体渠道。]
plotDensities(MA.n,arrays=NULL,groups=NULL,col=c("blue","purple"))
# Indexing individual-channels using singlechannels (arrays=NULL).[索引个别通道使用singlechannels（数组=空）。]
plotDensities(MA.n,singlechannels=c(1,2,7))
# Change the default colors from c("red","green") to c("pink","purple")[从C（“红”，“绿色”）更改默认的颜色为C（“粉红色”，“紫色”）]
plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple"))
# Specified too many colors since groups=NULL defaults to two groups.[指定了太多的色彩，因为组两组空默认。]
plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple","blue"))
# Three individual-channels, three groups, three colors.[三个独立的通道，三组，三色。]
plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,2,3),
col=c("pink","purple","blue"))
# Three individual-channels, one group, one color.[三个独立的通道，其中一组，一个颜色。]
plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,1,1),
col=c("purple"))
# All individual-channels, three groups (ctl,tmt,reference), three colors.[所有个人渠道，三组（CTL，TMT，仅供参考），三种颜色。]
plotDensities(MA.n,singlechannels=c(1:12),
groups=c(rep(1,3),rep(2,3),rep(3,6)),col=c("darkred","red","green"))
## End(Not run)[＃结束（不运行）]
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 23:21:35
