plotChimericReads(R453Plus1Toolbox)
plotChimericReads()所属R语言包：R453Plus1Toolbox
Plots chimeric reads
图嵌合读取
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function plots a given set of aligned chimeric reads along a reference sequence. It plots the breakpoints of translations or
这个函数绘出给定的对齐嵌合沿着参考序列读取。图翻译的断点或
用法----------Usage----------
参数----------Arguments----------
参数：brpData
A Breakpoints object containing the consensus breakpoint of all reads and the consensus reference sequence as returned by the methods detectBreakpoints and mergeBreakpoints. Since only one plot is made, the function will only work for objects of class Breakpoints having length one.
方法返回一个Breakpoints对象包含所有读取的共识断点和共识的参考序列detectBreakpoints和mergeBreakpoints。由于只有一个图是，该功能仅适用于类对象Breakpoints有一个长度。
参数：geneSymbols
Boolean value whether to automatically load and plot the gene symbols from the Ensembl database. Additionally, geneSymbols can be a vector of two strings for an own annotation.
布尔值是否自动加载并绘制从Ensembl的数据库中的基因符号。此外，geneSymbols可以是一个向量两串为自己的注解。
参数：plotMut
Boolean value whether to mark deletions, insertions and mismatches.
布尔值是否标示缺失，插入和不匹配。
参数：plotBasePairs
Optionally, plotChimericReads displays all base pairs in a given region around the breakpoint (see maxBasePairs).
（可选），plotChimericReads显示中断点周围区域的所有碱基对（见maxBasePairs）。
参数：maxBasePairs
The maximum number of base pairs to be plotted. Only used in conjunction with plotBasePairs=TRUE.
要绘制的最大数量的碱基对。只用plotBasePairs=TRUE一起使用。
参数：legend
A logical value (TRUE/FALSE) whether to plot a legend that explains the colouration of the insertions, deletions, mismatches and breakpoints.
逻辑值（TRUE / FALSE），是否要绘制一个传说，解释了着色的插入，删除，不匹配和断点。
参数：title
A title for the plot.
图的标题。
参数：col
A vector of four colours to draw insertions, deletions, mismatches and breakpoints. In this order, the default colours are "red", "green", "black" and "orange" (use colours() to see a list of possible values).
四种颜色绘制插入，删除，不匹配和断点向量。在这种秩序中，默认的颜色是“红”，“绿色”，“黑”和“橙色”（使用colours()看到一个可能值的列表）。
Details
详情----------Details----------
This method is intended to be run after the pipeline for structural variant detection. Therefore, see the methods filterChimericReads, detectBreakpoints and mergeBreakpoints to correctly preprocess your alignment before running plotChimericReads.
此方法的目的后的结构变异检测管道运行。因此，看到的方法filterChimericReads，detectBreakpoints和mergeBreakpoints运行plotChimericReads之前正确预处理对齐。
注意----------Note----------
It is recommended to first create and resize the output device (e.g. the plotting window or a pdf file) before plotting. For example, on Unix systems you may try X11(width=w, height=h) or pdf(file="plotChimericReads.pdf", width=w, height=h) for some window width w (e.g. w=12) and window height h (e.g. h=6).
它建议首先创建和调整前策划的输出设备（例如绘图窗口或PDF文件）。例如，在Unix系统上，你可以尝试X11(width=w, height=h)或pdf(file="plotChimericReads.pdf", width=w, height=h)一些窗口的宽度W（如W = 12）和窗口高度h（如H = 6）。
作者（S）----------Author(s)----------
Christoph Bartenhagen
参见----------See Also----------
Breakpoints-class, detectBreakpoints, mergeBreakpoints
Breakpoints-class，detectBreakpoints，mergeBreakpoints
举例----------Examples----------
# load breakpoint data containing twelve chimeric reads describing an inversion in chromosome 16[含有12嵌合负载断点数据读取描述在16号染色体的一个反转]
data("breakpoints")
breakpoints
# standard plot [标准样地]
# (only arrangement of reads plotted; breakpoints in orange, deletions[（只读取安排策划;橙色断点，删除]
# in red, insertions in green and mismatches in black by default)[在红色，绿色的插入和默认情况下，在黑色的不匹配）]
plotChimericReads(breakpoints)
# plot base pairs in the breakpoint region (+/- 32bp) [断点区域的地积碱基对（+ / - 32bp）]
## Not run: plotChimericReads(breakpoints, plotBasePairs=TRUE, maxBasePairs=32)[＃运行：plotChimericReads（断点plotBasePairs = TRUE时，maxBasePairs = 32）]
# use custom colours and display a legend:[使用自定义的颜色，并显示一个传说：]
# deletions="brown", insertions="blue", mismatches="yellow", breakpoints="gray"[删除=“褐色”，插入=“蓝”，不匹配的“黄色”，断点“灰色”]
plotChimericReads(breakpoints, col=c("brown", "blue", "yellow", "gray"), legend=TRUE)
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 2012-2-26 11:51:25
