plot.job(BayesPeak)
plot.job()所属R语言包：BayesPeak
Plot the called peaks in a job.
绘制工作的所谓峰。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plot the distribution of reads in a .bed file, with BayesPeak's calls highlighted.
绘制分布。床上文件中读取，突出与BayesPeak的呼声。
用法----------Usage----------
plot.job(x, raw.out, job, strand = "+", threshold = 0.5,
xlim = c(0,1), highlight = TRUE, col.un = "grey",
col.enr = "blue", bin = 100L, ...)
参数----------Arguments----------
参数：x
RangedData (from the IRanges package) with a value column entitled "strand". The .bed file to plot. This could have been read in with read.bed, or alternatively by the import function in the rtracklayer library.
RangedData（从IRanges包）的值列题为"strand"。图。床文件。这可能已经读取read.bed，或者import在rtracklayer库功能。
参数：raw.out
Raw output from the bayespeak function.
从原料输出bayespeak功能。
参数：job
Integer. The number of the job to plot.
整数。作业的数量积。
参数：strand
Character. Strand to plot - usually either "+" or "-". If the bed argument uses a different convention in its strand column, this can be used instead.
字符。链图 - 通常不是“+”或“ - ”。如果bed参数使用不同的约定，在其股列，这可以用来代替。
参数：threshold
Numeric. Bins with a PP higher than this value will be classed as enriched.
数字。这个值比聚丙烯高的垃圾桶，将被归类为丰富。
参数：xlim
Numeric vector. This controls which part of the job is plotted. For example, c(0.5,1) would plot the last half of the job, whereas c(0.25,0.75) would plot the central half.
数字向量。这控制绘制工作的一部分。例如，c(0.5,1)将绘制工作的最后一半，而c(0.25,0.75)将绘制中央的一半。
参数：highlight
Logical. FIXME
逻辑。 FIXME
参数：col.un
The colour used to plot counts in unenriched bins.
颜色用于图计数unenriched箱。
参数：col.enr
The colour used to plot counts in enriched bins.
图丰富箱计数的颜色。
参数：bin
What sized bin should be used? Currently, this value should be the same as the value used in bayespeak. The function will behave strangely if this parameter is altered, particularly to pathological values.
应使用中型斌，怎么办？目前，这个值应该是作为bayespeak使用的值相同。该函数将行为很奇怪，如果这个参数被改变，尤其是病理值。
参数：...
Additional arguments to be passed through to hist.
额外的参数，可以通过hist。
Details
详情----------Details----------
Similar to plot.bed, plot.job takes the reads in a bed file, and plots a histogram of their locations - i.e. plots the bin counts. It then goes on to highlight the histogram bins that have been made in the raw.output from bayespeak.
类似plot.bed，plot.job需要的在床上文件读取，并绘制直方图的位置 - 即图的bin计数。接着上突出直方图箱已在从bayespeakraw.output。
It is worth bearing in mind that BayesPeak takes the information on both strands into account when calling peaks, and therefore judgements based on a one-stranded view of the data should be treated with caution. For a better picture of what is going on, both strands should be viewed simultaneously, as is done in the examples below.
这是值得铭记，BayesPeak考虑到两个链上的信息时，调用峰，因此判断的数据链的基础上，应谨慎对待。为更好的画面是怎么回事，应同时观看两个链，为的是在下面的例子。
值----------Value----------
Plots a histogram on the active graphical device.
绘制直方图上活跃的图形设备。
作者（S）----------Author(s)----------
Jonathan Cairns
参考文献----------References----------
BayesPeak: Bayesian analysis of ChIP-seq data, BMC Bioinformatics 2009, 10:299 doi:10.1186/1471-2105-10-299
参见----------See Also----------
bayespeak, read.bed, plot.bed.
bayespeak，read.bed，plot.bed。
举例----------Examples----------
##get the ChIP .bed file[＃得到床文件的芯片。]
dir <- system.file("extdata", package="BayesPeak")
treatment <- file.path(dir, "H3K4me3reduced.bed")
bed <- read.bed(treatment)
##get the corresponding raw.output object[＃得到相应raw.output对象。]
data(raw.output.H3K4me3)
##plot job 1, + and - strand[＃积工作1 + - 链]
par(mfrow = c(2,1))
plot.job(bed, raw.output.H3K4me3, 1)
plot.job(bed, raw.output.H3K4me3, 1, "-")
##zoom in for a closer look...[＃放大细看...]
plot.job(bed, raw.output.H3K4me3, 1, xlim = c(0.58,0.6))
plot.job(bed, raw.output.H3K4me3, 1, "-", xlim = c(0.58,0.6))
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 12:30:38
