plotGenome(segmentSeq)
plotGenome()所属R语言包:segmentSeq
Plots the alignment of sequence tags on the genome given an ‘aligmentData’ object and (optionally) a set of segments found.
图“aligmentData对象(可选)发现段的基因组序列标签对齐。
译者:生物统计家园网 机器人LoveR
描述----------Description----------
Plots the data from an alignmentData object for a given set of samples. Can optionally include in the plot the annotation data from a lociData object containing segment information.
图为给定的样本数据,从alignmentData对象。可以选择包括在图从lociData对象,其中包含部分信息的注释数据。
用法----------Usage----------
plotGenome(aD, locData, chr = 1, limits = c(0, 1e4), samples = NULL,
plotType = "pileup", plotDuplicated = FALSE, density = 0, showNumber =
TRUE, logScale = FALSE, cap = Inf, ...)
参数----------Arguments----------
参数:aD
An alignmentData object.
alignmentData对象。
参数:locData
A lociData object (produced by the heuristicSeg or classifySeg function and therefore) containing appropriate annotation information. Can be omitted if this annotation is not known/required.
一个lociData对象(heuristicSeg或classifySeg函数,因此产生的),包含相应的注释信息。不知道/如果这个注解可以省略。
参数:chr
The name of the chromosome to be plotted. Should correspond to a chromosome name in the alignmentData object.
染色体的名称要绘制。应该对应一个染色体在alignmentData对象名称。
参数:limits
The start and end point of the region to be plotted.
该区域的起点和终点绘制。
参数:samples
The sample numbers of the samples to be plotted. If NULL, plots all samples.
样本的样本数要绘制。如果为NULL,所有样品图。
参数:plotType
The manner in which the plot is created. Currently only plotType = pileup is recommended.
在其中创建该图的方式。目前只有plotType = pileup建议。
参数:plotDuplicated
If TRUE, then any duplicated sequence tags (i.e., sequence tags that match to multiple places in the genome) in the "aD" object will be plotted on a negative scale for each sample. Defaults to FALSE (recommended).
如果TRUE,那么任何重复序列标签(即基因组中的多个地方匹配的序列标签)在“广告”对象将绘制在每个样品负的规模。默认为FALSE(推荐)。
参数:density
The density of the shading lines to be used in plotting each segment.
阴影线的密度,以用于绘制各分部。
参数:showNumber
Should the row number of each segment be shown?
各段的显示行数吗?
参数:logScale
Should a log scale be used for the number of sequence tags found at each base?
log的规模应该被用于在每个碱基的序列标签的数量?
参数:cap
A numeric value defining a cap on the maximum number of reads to be plotted at any one point. Useful if a large number of reads at one location prevent a clear signal being seen elsewhere.
读取在任何一个点绘制的数值定义的最大数量的上限。有用的,如果在一个位置的读取大量防止被其他地方看到一个明确的信号。
参数:...
Any additional graphical parameters for passing to plot.
任何额外的图形参数传递给plot。
值----------Value----------
Plotting function.
绘图功能。
作者(S)----------Author(s)----------
Thomas J. Hardcastle
参见----------See Also----------
alignmentData, heuristicSeg, classifySeg
alignmentData,heuristicSeg,classifySeg
举例----------Examples----------
# Define the chromosome lengths for the genome of interest.[定义感兴趣的基因组染色体长度。]
chrlens <- c(2e6, 1e6)
# Define the files containing sample information.[定义文件包含样本信息。]
datadir <- system.file("extdata", package = "segmentSeq")
libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")
# Establish the library names and replicate structure.[建立图书馆的名称和复制结构。]
libnames <- c("SL9", "SL10", "SL26", "SL32")
replicates <- c(1,1,2,2)
# Process the files to produce an `alignmentData' object.[处理文件,以生产alignmentData“对象。]
alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
replicates, libnames = libnames, chrs = c(">Chr1", ">Chr2"), chrlens =
chrlens, gap = 100)
# Plot the alignments to the genome on chromosome 1 between bases 1 and 10000[碱基1和10000之间的1号染色体上的基因组绘制的路线]
plotGenome(alignData, chr = ">Chr1", limits = c(1, 1e5))
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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