chipAlongChrom(Ringo)
chipAlongChrom()所属R语言包：Ringo
Visualize ChIP intensities along the chromosome
沿染色体芯片强度的可视化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function can visualize the array intensities from a ChIP chip experiment for a chromosomal region or the whole chromosome. It's based on the plotAlongChrom function from the package tilingArray, but provides a different visualization.
此功能可以从一个染色体区域或整个染色体芯片芯片实验可视化阵列的强度。它是基于plotAlongChrom包tilingArray的功能，但提供了一个不同的可视化。
用法----------Usage----------
## S4 method for signature 'ExpressionSet,probeAnno'
plot(x, y, ...)
chipAlongChrom(eSet, probeAnno, chrom, xlim, ylim,
samples = NULL, paletteName = "Set2", colPal = NULL,
ylab = "Fold change [log]", ipch = 16, ilwd = 3, ilty = 1,
icex = 3, gff = NULL,
featureExclude=c("chromosome", "nucleotide_match","insertion"),
zeroLine = TRUE, sampleLegend = TRUE, sampleLegendPos = "topleft",
featureLegend = FALSE, maxInterDistance = 200, coord = NULL,
highlight, main, ...)
参数----------Arguments----------
参数：eSet
An expression set containing the (normalized) ChIP intensities, e.g. the result objects from functions preprocess and computeRunningMedians.
（归）芯片的强度，例如表达式集从功能preprocess和computeRunningMedians结果的对象。
参数：x
Corresponds to argument eSet when calling the S4 method
对应的参数eSet调用时的S4方法
参数：probeAnno
An object of class probeAnno holding genomic position, index and gene association of probes on array.
类probeAnno控股基因组的位置，索引阵列探针和基因关联的对象。
参数：y
Corresponds to argument probeAnno when calling the S4 method
对应的参数probeAnno调用时的S4方法
参数：chrom
character; the chromosome to visualize
字符;染色体可视化
参数：xlim
start and end genomic coordinates on the chromosome to visualize
开始和结束在染色体上的基因坐标可视化
参数：ylim
minimum and maximum probe intensities for the plot, if missing (default) set to range(exprs(eSet))
图最大和最小的探针强度，如果缺少（默认）设置range(exprs(eSet))的
参数：samples
numeric; which samples from the eSet are to be shown. Default is to show all samples in the eSet,
数字;样品从eSet显示。默认是显示所有的样品在eSet
参数：paletteName
character; Name of the RColorBrewer palette to use for sample colors. If the number of samples is greater than the palette size, random colors are taken.
字符;名的RColorBrewer调色板用于样品颜色。如果样本数大于调色板的大小，采取随机颜色。
参数：colPal
vector of colors to use for the sample intensities. This is alternative to the argument paletteName for specifying which colors to use.
向量的颜色用于样品的强度。这是替代参数paletteName指定使用的颜色。
参数：ylab
character; label for the y-axis, passed on to the plotting function as ylab
字符;为y轴的标签，通过绘图函数ylab
参数：ipch
plot character to use
图字符使用
参数：icex
character expansion to use for plotting symbol
字符扩展到用于绘制符号
参数：ilwd
line width of plotted data lines
绘制数据线线宽
参数：ilty
line type of plotted data lines; passed on to par(lty).
绘制线类型数据线;传递par(lty)的。
参数：gff
data frame containing annotation for genomic feature to be used to further annotate the plot.
数据框包含的基因组功能注释被用来进一步注解的图。
参数：featureExclude
character vector specifying the feature types in the data.frame gff that should not be shown in the plot
指定在数据框的特征类型的特征向量gff这不应该被显示在图
参数：zeroLine
logical; should a dashed horizontal line at y=0 be put into the plot?
逻辑;应在y = 0的水平线虚线投入图吗？
参数：sampleLegend
logical; should a sample legend be put into the plot?
逻辑;应该样品传说被放入图吗？
参数：sampleLegendPos
character; where to put the sample legend; one of "topleft" (default), "bottomleft", "topright", or "bottomrigth"
字符;把样品传说“左上”（默认），“bottomleft，topright，或bottomrigth;
参数：featureLegend
logical; should a feature legend be put beneath the plot?
逻辑;的功能图例下方的图吗？
参数：maxInterDistance
numeric; only used when itype is either "r" or "u"; specifies the maximal distance up to which adjacent probe positions should be connected by a line.
数字时只用了itype“R”或“U”;指定相邻的探针位置应连接线的最大距离。
参数：coord
optional integer of length 2; can be used instead of xlim to specify the start and end coordinates of the genomic region to plot
可选的整数长度为2;可以用来代替xlim指定的基因组区域的开始和结束坐标绘制
参数：highlight
optional list specifying a genomic region to be highlighted in the shown plot
可选列表指定一个基因区域在所示图突出
参数：main
optional main title for the plot; if not specified: the default is "Chromosome coordinate [bp]"
可选的主标题的图;如果没有指定，默认为“染色体坐标[BP]
参数：...
further parameters passed on to grid.polyline and grid.points
通过进一步的参数grid.polyline和grid.points
值----------Value----------
invisible list of probe positions (element x) and probe levels (element y) in the selected genomic region.
invisible探针位置的列表（元素x）和探测水平（元素y）在选定的基因组区域。
注意----------Note----------
The S4 method is provided as a mere convenience wrapper.
S4的方法是仅仅作为一种方便的包装。
When plotting a new "grid" plot in an active x11 window that already contains a plot, remember to call grid.newpage() before.
策划一个新的“网格”在一个活跃的X11窗口，已经包含了一个图的图时，记得打检测grid.newpage()之前。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
ExpressionSet-class, probeAnno-class, grid.points,
ExpressionSet-class，probeAnno-class，grid.points
举例----------Examples----------
### load data[＃＃加载数据]
ringoExampleDir <- system.file("exData",package="Ringo")
load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
load(file.path(ringoExampleDir,"exampleX.rda"))
### show a gene that is well represented on this microarray[＃显示，此芯片为代表的基因]
plot(exampleX, exProbeAnno, chrom="9",
xlim=c(34318000,34321000), ylim=c(-2,4), gff=exGFF)
### this should give you the same result as:[＃＃这应该给你相同的结果：]
chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)
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 12:56:42
