plot.DNAcopy(DNAcopy)
plot.DNAcopy()所属R语言包：DNAcopy
Plot the data and results from segment of a CNA object
图从一个CNA对象段的数据和结果
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plots the data from a copy number array experiment (aCGH, ROMA etc.) along with the results of segmenting it into regions of equal copy numbers.
图从拷贝数阵列实验，随着区域平等的拷贝数分割成的结果（aCGH，罗马等）的数据。
用法----------Usage----------
## S3 method for class 'DNAcopy'
plot(x, plot.type=c("whole", "plateau", "samplebychrom",
"chrombysample"), xmaploc=FALSE, altcol=TRUE, sbyc.layout=
NULL, cbys.nchrom=1, cbys.layout=NULL, include.means=TRUE,
zeroline=TRUE, pt.pch=NULL, pt.cex=NULL, pt.cols=NULL,
segcol= NULL, zlcol=NULL, ylim=NULL, lwd=NULL, ...)
参数----------Arguments----------
参数：x
an object of class DNAcopy resulting from analyzing data from copy number array experiments.
一个类的对象DNAcopy从造成套数阵列实验数据分析。
参数：plot.type
the type of plot.
图类型。
参数：xmaploc
logical flag to indicate that the X axis is the maploc position rather than the index. Since the segments are rearranged the plateau plot does not use maploc position.
逻辑标志来表明，X轴是指数，而不是maploc位置。由于段重新排列高原图不使用maploc位置。
参数：altcol
logical flag to indicate if chromosomes should be plotted in alternating colors in the whole genome plot.
逻辑标志来表明，如果染色体应交替颜色在整个基因组的图策划。
参数：sbyc.layout
layout settings for the multifigure grid layout for the "samplebychrom" type. It should be specified as a vector of two integers which are the number of rows and columns. The default values are chosen based on the number of chromosomes to produce a near square graph. For normal genome it is 4x6 (24 chromosomes) plotted by rows.
layout设置为“samplebychrom型multifigure网格布局。它应该被指定为两个整数的行和列数的向量。选择默认值的染色体数目的基础上产生一个近正方形图。对于正常的基因，它是4X6（24染色体）按行绘制。
参数：cbys.layout
layout settings for the multifigure grid layout for the "chrombysample" type. As above it should be specified as number of rows and columns and the default chosen based on the number of samples.
layout设置为“chrombysample型multifigure网格布局。如上所述，它应该被指定为行和列的数目，默认选择的样本数量的基础上。
参数：cbys.nchrom
the number of chromosomes per page in the layout. The default is 1.
在布局中的的每页染色体数目。默认值是1。
参数：include.means
logical flag to indicate whether segment means are to be drawn.
逻辑标志来表明是否是要绘制的部分手段。
参数：zeroline
logical flag to indicate whether a horizontal line at y=0 is to be drawn.
逻辑标志来表明是否将被绘制在Y = 0的水平线是。
参数：pt.pch
the plotting character used for plotting the log-ratio values (default is ".").
用于绘图log比率值（默认为“。”）绘制字符。
参数：pt.cex
the size of plotting character used for the log-ratio values (default is 3).
log比率值（默认为3）用于绘制字符的大小。
参数：pt.cols
the color list for the points. The colors alternate between chromosomes. If missing the point colors are black and green.
点的颜色列表。染色体之间的交替颜色。如果缺少点的颜色是黑色和绿色。
参数：segcol
the color of the lines indicating the segment means. If missing the line color is set to be red.
说明段的线的颜色是指。如果缺少线条颜色设置为红色。
参数：zlcol
the color of the zeroline. If missing it is set to be grey.
颜色的zeroline。如果缺少它被设置为灰色。
参数：ylim
this argument is present to override the default limits which is the range of symmetrized log-ratios.
这种说法是目前覆盖默认的限制，这是对称log比率的范围。
参数：lwd
line weight of lines for segment mean and zeroline. If missing it is set to 3.
线路段线的重量意味着zeroline。如果缺少它被设置为3。
参数：...
other arguments which will be passed to plot commands.
这将传递给plot命令的其他参数。
Details
详情----------Details----------
There are four possible plot types. For the type "whole" the data are plotted for the entire genome. For the "samplebychrom" type a graph with each chromosome (of a given sample) is drawn in a separate figure on a multi-figure grid. For the "plateau" type the graph is drawn with the chromosome segments re-ordered by the segment means. For the "chrombysample" type the samples for a given chromosome are drawn in a 4x6 multi-figure grid in multiples of 24. By default the segments means are drawn. For multisample data each sample or chromosome is drawn on a separate sheet. When invoked interactively the user is prompted before advancing to the next sample.
有四种可能的图类型。型全的数据绘制了整个基因组。为的“samplebychrom型，每个染色体（一个给定的样本）的图形绘制在一个多图格独立的数字。为“高原型图绘制段重新排序是指染色体片段。对于一个给定的染色体样本为的“chrombysample型绘制在一个4x6的多图格24的倍数。默认情况下，细分手段绘制。对于多重采样数据，每个样品或染色体上绘制一个单独的表。交互式的调用时会提示用户，然后推进到下一个样品。
举例----------Examples----------
#Read in two examples from Snijders et al.[阅读斯奈德斯等的两个例子。]
data(coriell)
#Combine into one CNA object to prepare for analysis on Chromosomes 1-23[结合成一个中央社的对象，准备进行分析，染色体1-23]
CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
coriell$Chromosome,coriell$Position,
data.type="logratio",sampleid=c("c05296","c13330"))
#We generally recommend smoothing single point outliers before analysis[我们一般建议在分析单点离群平滑]
#Make sure to check that the smoothing is proper[确保检查是正确的平滑]
smoothed.CNA.object <- smooth.CNA(CNA.object)
#Segmentation at default parameters[在默认参数的分割]
segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1)
#Plot whole studies[绘制整个研究]
plot(segment.smoothed.CNA.object, plot.type="w")
#Plot each study by chromosome[绘制每个染色体研究]
plot(segment.smoothed.CNA.object, plot.type="s")
#Plot each chromosome across studies (6 per page)[绘制相望研究染色体（每6页）]
plot(segment.smoothed.CNA.object, plot.type="c", cbys.layout=c(2,1), cbys.nchrom=6)
#Plot by plateaus[图高原]
plot(segment.smoothed.CNA.object, plot.type="p")
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 16:42:17
