plotAlongChrom(tilingArray)
plotAlongChrom()所属R语言包：tilingArray
Plot signals and segmentation for a region of a chromosome
图信号和染色体区域分割
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plot signals and segmentation for a region of a chromosome
图信号和染色体区域分割
用法----------Usage----------
plotAlongChrom(segObj, y, probeAnno, gff,
isDirectHybe=FALSE,
what = c("dots"), ## "heatmap"
chr, coord, highlight,
colors, doLegend=FALSE,
featureExclude=c("chromosome", "nucleotide_match", "insertion"),
featureColorScheme=1, extras,
rowNamesHeatmap, rowNamesExtras, ylab, ylabExtras, main,
colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")),
colExtras=colorRamp(brewer.pal(9, "Reds")),
sepPlots=FALSE, reOrder=TRUE, ...)
参数----------Arguments----------
参数：segObj
Either an environment or an object of S4 class segmentation. See Details.
无论是环境或一个S4类segmentation对象。查看详细信息。
参数：y
a numeric vector or matrix containing the signal to be plotted. See Details.
包含信号的数字向量或矩阵绘制。查看详细信息。
参数：probeAnno
environment with probe annotations. See Details, and package davidTiling for an example.
环境探针注释。详情，包davidTiling一个例子。
参数：gff
data frame with genome annotation from the GFF file.
从GFF文件与基因组注释的数据框。
参数：isDirectHybe
logical scalar: if TRUE, the mapping of probes to genomic strands is reversed with respect to the default. This is appropriate for data from a direct RNA hybridization that used no reverse transcription.
标逻辑：如果为TRUE，探针到基因链的映射默认逆转。这是适合于从直接的RNA杂交，没有使用反转录的数据。
参数：what
character scalar indicating which signal visualization to plot. Can be either dots to plot each probe intensity with a point, or heatmap to produce a colorscale representation of the intesities.
字符标指示绘制的信号可视化。可以要么dots点绘制每个探针的强度，或heatmap以产生的intesities的colorscale的代表。
参数：chr
integer of length 1 indicating the chromosome number to plot.
长度指示的染色体数目积1的整数。
参数：coord
integer vector of length 2 containing the start and end coordinates (in bases) for the plot.
长度为2的整数向量积的坐标（碱基）的开始和结束。
参数：highlight
(optional) list with two elements: a single numeric value coord and a character strand. If present, this position is marked by a vertical red bar on the coordinate axis. The color can be changed using the colors argument below.
（可选）列表中有两个元素：一个数值coord和一个字符strand。如果存在，这个位置标明由一个垂直的坐标轴的红色条。使用下面的colors参数，可以改变颜色。
参数：colors
(optional) named character vector. If missing, a default color scheme is used: c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey"), where the first three elements refer to the colors of data points and the last three to the colors of lines in the plot.
（可选）命名的特征向量。如果缺少，默认颜色方案：c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey")，其中前三个要素是指数据点的颜色和过去三年中的图线的颜色。
参数：doLegend
logical: should the plot contain a legend?
逻辑：图应该包含一个传说吗？
参数：featureExclude
character vector of names of feature types (in gff) that should not be plotted. Default is "chromosome", "nucleotide_match" and "insertion". Additional possibilities include: "ARS", "repeat\_region", "repeat\_family" and "nc\_primary\_transcript".
特征向量的特征类型的名称不应该被绘制（gff）。默认是"chromosome""nucleotide_match"和"insertion"。其他可能性包括："ARS"，"repeat\_region"，"repeat\_family"和"nc\_primary\_transcript"。
参数：featureColorScheme
numeric scalar, used to select a color scheme for the boxes representing genomic features such as coding sequences, ncRNAs etc. Currently the only value supported is 1 (see plotAlongChromLegend or plotFeatures for further information).
数字标量，用于选择配色方案为代表盒基因的功能，如编码序列，非编码RNA等目前支持的唯一的价值是1（见plotAlongChromLegend或plotFeatures为进一步的信息）。
参数：extras
a matrix containing additional values to be plotted along the chromosome in a separate panel (such as p-values). This option is only available when y is specified. These values should be on the scale [0,1].
要绘制一个矩阵包含的附加价值沿染色体在一个单独的面板（如p值）。此选项仅当y指定。这些值应该是上规模[0,1]。
参数：rowNamesHeatmap
character vector of row names for the main heatmap.
特征向量为主要热图的行名。
参数：rowNamesExtras
character vector of row names for the extra heatmap.
额外的热图行名称的特征向量。
参数：ylab
character label for y-axis of main plot.
主要图Y轴的性格标签。
参数：ylabExtras
character label for y-axis on extras panel (if specified).
extras面板（如果指定）Y轴的性格标签。
参数：main
character: plot title.
性格：小区称号。
参数：colHeatmap
function describing color scheme for the main heatmap plot (defaults to YlGnBu from RColorBrewer package).
功能描述图（从RColorBrewer包默认YlGnBu）为主要热图的配色方案。
参数：colExtras
function describing color scheme for the extra heatmap plot (if specified) (defaults to Reds from RColorBrewer package).
功能描述额外的热图图的配色方案（如果指定）（默认为Reds的RColorBrewer包）。
参数：sepPlots
logical scalar. If TRUE, each column of intensities in segObj or y is plotted separately (maximum of 3) in the same figure. When FALSE, the average is plotted. This argument is only used when what is set to dots.
逻辑标量。如果是TRUE，每列segObj或y分别绘制在同一图最多（3）强度。如果为FALSE，平均绘制。这种说法只用来当what设置为dots。
参数：reOrder
logical scalar (only used when sepPlots is TRUE). If TRUE, the first column of intensities is printed at the bottom of each plot, and the subsequent columns are plotted above. If FALSE, the first appears at the top, and the subsequent columns are plotted below.
逻辑标量（仅用于当sepPlots为TRUE）。如果是TRUE，第一列的强度是印在每个小区的底部，随后列上面绘制。如果为FALSE，首先出现在顶部，随后列下面的绘制。
参数：...
further arguments that can be passed to the functions that implement the what option above (see plotSegmentationDots and plotSegmentationHeatmap) or gff plotting (see plotFeatures and plotAlongChromLegend).
可以通过进一步论据的职能，落实what以上选项（见plotSegmentationDots和plotSegmentationHeatmap）gff绘制（见plotFeatures和plotAlongChromLegend）。
Details
详情----------Details----------
Intensities: There are two alternative, mutually exclusive ways of providing the intensities that are to be plotted to this function.
强度：有两个替代，相互排斥的方式提供强度，绘制此功能。
Via the parameters y and probeAnno. In this case, y is a matrix of intensities, whose rows correspond to probes on the array, and its columns to different conditions, time points, etc. It is also acceptable that y is provided as a vector, in which case it is converted to an nrow(y) x 1 matrix. probeAnno is an environment whose elements correspond to target sequences (e.g. chromosome strands) and that contain integer vectors of length nrow(y) with information about the probes: start and end positions of their alignment to the target sequence, their row indices in y, the type of alignment (is it perfect? is is unique?). For example, the start positions and indices of probes for the + strand of chromosome 1 would be described by environment elements "1.+.start" and "1.+.index".
通过参数y和probeAnno。在这种情况下，y强度矩阵的行对应于阵列上的探针，其列不同的条件，时间点等，这也是可以接受的y作为提供向量，在这种情况下，它被转换为nrow(y) x 1矩阵。 probeAnno是一个环境，对应于靶序列（如染色体股），包含整数长度nrow(y)探针的信息向量：其对齐的开始和结束位置的靶序列，其元素行指数在y，对齐类型（它是完美的吗？是唯一的吗？）。例如，将探针+ 1号染色体链的起始位置指数由环境因素描述"1.+.start"和"1.+.index"。
Via the parameter segObj.
通过参数segObj。
segObj: This can be either an object of S4 class segmentation or an environment that by convention contains a certain set of objects. Future work on this package will focus on the S4 class segmentation. The environment option is provided for backward compatibility.
segObj：这可以是一个S4类segmentation或环境的对象，按照惯例，包含一定的对象。关于这个软件包的未来工作将侧重于在S4级segmentation。 environment选项提供向后兼容性。
Explanation of the environment: the intended workflow is as follows: Use the script segment.R (in the inst/scripts directory of this package) to generate segmentations. This can be run in parallel on several processors, separately for each chromosome and strand. The results of this are stored in files of the name 1.+.rda, 1.-.rda, 2.+.rda, and so forth, typically within a dedicated directory. Then use the script readSegments.R to collect the R objects in these .rda files into the environment. It contains three types of data:
环境说明：预定的工作流程如下：使用脚本segment.R（inst/scripts这个包的目录）产生区隔。这可以在多个处理器上并行运行，分别为每个染色体和钢绞线。这个结果存储在文件名称中的1.+.rda，1.-.rda，2.+.rda，等等，通常在一个专用的目录。然后使用脚本readSegments.R在这些R到环境中的文件中收集的.rda的对象。它包含三种类型的数据：
microarray intensities in along-chromosome order.
芯片在沿染色体为了强度。
the segmentation objects (output of findSegments).
分割的对象（输出的findSegments）。
a dataframe named segScore with segment scores; it can be missing iff nrBasesPerSeg is present,
1 dataframe名为segScore段分数，它可以缺少IFFnrBasesPerSeg目前，
a numeric scalar names theThreshold, which is used to draw a horizontal "threshold" line in the plot.
数字标名theThreshold，这是用来绘制水平的“阈值”在图线。
... and the different signal visualization methods (what option): If what=="dots", the argument showConfidenceIntervals can be a logical scalar to choose whether vertical dashed lines are drawn for the confidence interval. In any case, these are only drawn if they are present in the segmentation object in segObj.
...和不同的信号可视化方法（what选项）：如果what=="dots"“的说法showConfidenceIntervals可以选择是否垂直虚线绘制的置信区间是一个逻辑标。在任何情况下，这些如果他们是在segmentationsegObj对象目前只绘制。
作者（S）----------Author(s)----------
Wolfgang Huber <huber@ebi.ac.uk>
举例----------Examples----------
## 1. see viewSegmentation.R script in the inst/scripts directory[＃1。 INST / scripts目录中看到viewSegmentation.R脚本]
## 2. (newer): segmentation.Rnw[＃2。 （新）：segmentation.Rnw]
## 3. (newer): see the plotALongChrom vignette[＃3。 （新）：看到plotALongChrom插曲]
data(segnf)
data(gffSub)
nmLabel = colnames(segnf$"1.+"@y)
plotAlongChrom(segnf,chr=1,coord=c(35000,50000),
gff=gffSub,rowNamesHeatmap=nmLabel) ##the dots[＃点]
plotAlongChrom(segnf,chr=1,coord=c(35000,50000),what="heatmap",
gff=gffSub,rowNamesHeatmap=nmLabel) ##the heatmap[＃的热图]
plotAlongChrom(segnf,chr=1,coord=c(35000,50000),gff=gffSub,
showConfidenceIntervals=FALSE) ##do not show the segment confidence interval [＃不显示段的置信区间]
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 15:34:56
