plotPeaks(nucleR)
plotPeaks()所属R语言包：nucleR
Nucleosome calling plot function
核小体的通话绘图功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Helper function for a quick and convenient overview of nucleosome calling data.
Helper函数为核小体的呼叫数据的快速，便捷的概述。
This function is intended to plot data previously processed with nucleR pipeline. It shows a coverage/intensity profile toghether with the identified peaks. If available, score of each peak is also shown.
此功能的目的是绘制以前nucleR管线处理的数据。它显示覆盖/强度剖面toghether的的一个确定的山峰。如果可用，每个高峰的得分也同时显示。
用法----------Usage----------
plotPeaks(peaks, data, ...)
## S4 method for signature 'IRanges'
plotPeaks(peaks, data, threshold=0, scores=NULL, start=1,
end=length(data),dyn.pos=TRUE, xlab="position", type="l", col.points="red",
thr.lty=1, thr.lwd="1", thr.col="darkred", rect.thick=2, rect.lwd=1,
rect.border="black", scor.col=col.points, scor.font=2, scor.adj=c(0.5,0),
scor.cex=0.75, scor.digits=2,...)
## S4 method for signature 'numeric'
plotPeaks(peaks, data, threshold=0, scores=NULL, start=1,
end=length(data), xlab="position", type="l", col.points="red",
thr.lty=1, thr.lwd="1", thr.col="darkred", scor.col=col.points, scor.font=2,
scor.adj=c(0.5,0), scor.cex=0.75, scor.digits=2,...)
参数----------Arguments----------
参数：peaks
numeric, data.frame, IRanges or RangedData object containing the detected peaks information. See help of peakDetection or peakScoring for more details.
numeric，data.frame，IRanges或RangedData对象，其中包含检测到的峰信息。看到peakDetection或peakScoring帮助更多的细节。
参数：data
Coverage or Tiling Array intensities
覆盖或平铺阵列强度
参数：threshold
Threshold applied in peakDetection
阈值应用peakDetection
参数：scores
If peaks is a data.frame or a RangedData it's obtained from 'score' column, otherwise, scores can be given here as a numeric vector
如果peaks是data.frame或RangedData它获得“得分”列，否则，scores可以给这里作为一个numeric向量
参数：start, end
Start and end points defining a subset in the range of data. This is a convenient way to plot only a small region of data, without dealing with subsetting of range or score objects.
开始和结束点定义的一个子集在data的范围内。这是一种方便的方法处理子集范围或得分的对象只是一个小的数据区域，绘制。
参数：dyn.pos
If peaks are ranges, should they be positioned dynamicaly on top of the peaks or staticaly at threshold baseline. Spacing of overlapping ranges is automatically applied if FALSE.
如果峰的范围，他们应该被定位dynamicaly峰顶部或staticalythreshold基线。间距是重叠的范围自动套用如果FALSE。
参数：xlab, type, col.points
Default values to be passed to plot and points
默认值将被传递给plot和points
参数：thr.lty, thr.lwd, thr.col
Default values to be passed to abline for threshold representation
默认值阈值表示要传递到abline
参数：rect.thick, rect.lwd, rect.border
Default values for rect representation or ranges. rect.thick indicates the thickness (in percentage relative to y-axis range) of the rectangles.
rect陈述或范围的默认值。 rect.thick表示的矩形厚度（Y轴范围相对百分比）。
参数：scor.col, scor.font, scor.adj, scor.cex, scor.digits
Default values for text representation for score numbers, if available.
text表示得分的数字，如果可用的默认值。
参数：...
Other parameters passed to plot function
其他参数传递给plot函数
值----------Value----------
(none)
（无）
作者（S）----------Author(s)----------
Oscar Flores <a href="mailto flores@mmb.pcb.ub.es">oflores@mmb.pcb.ub.es</a>
参见----------See Also----------
peakDetection, peakScoring, plot,
peakDetection，peakScoring，plot
举例----------Examples----------
#Generate a random peaks profile[生成一个配置文件随机峰]
reads = syntheticNucMap(nuc.len=40, lin.len=130)$syn.reads
cover = coverage(reads)
#Filter them[过滤网]
cover_fft = filterFFT(cover)
#Detect peaks[检测峰]
peaks = peakDetection(cover_fft, threshold="40%", score=TRUE, width=140)
#Plot peaks and coverage profile (show only a window)[积峰和覆盖的文件（只显示一个窗口）]
plotPeaks(peaks, cover_fft, threshold="40%", start=1000, end=6000)
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 2012-2-26 07:55:26
