plotSegmentationHeatmap(tilingArray)
plotSegmentationHeatmap()所属R语言包：tilingArray
Plot a heatmap diagram for a region along a chromosome
绘制沿染色体的一个区域热图图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plot a heatmap diagram for a region along a chromosome
绘制沿染色体的一个区域热图图
用法----------Usage----------
plotSegmentationHeatmap(dat, xlim, ylab, rowNames,
chr=1, strand="+", vpr, colors,
colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")),
showConfidenceIntervals=TRUE,
just=c("left","centre"),
main,makeRasterImage = TRUE, ...)
参数----------Arguments----------
参数：dat
list containing data to be plotted (see Details section below for particulars).
列出包含要绘制的数据（见详图以下为详情）。
参数：xlim
integer vector of length 2 with start and end coordinates (in bases) for plotting.
整数向量的长度与绘图的起点和终点的坐标（碱基）2。
参数：ylab
character scalar specifying y-axis label.
指定Y轴标签的字符标。
参数：rowNames
character vector specifying a name for each row in the heatmap plot.
特征向量在热图图的每一行指定一个名称。
参数：chr
integer of length 1 indicating the chromosome to plot (defaults to 1).
长度为1的整数，指示绘制的染色体（默认为1）。
参数：strand
character scalar which should be set to either + or - to indicate which strand of DNA to plot the intensity values from (defaults to "+").
应设置的字符标要么+或-指示绘制的DNA链的强度值（默认值+“）。
参数：vpr
which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing.
视口绘制图，如果这种说法应留待失踪的用户直接调用此函数。
参数：colors
named character vector, optional. 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 colors of data points and the last three to those of lines in the plot.
命名的特征向量，可选。如果缺少，默认颜色方案：c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey")，其中前三个元素是指数据点的颜色和过去三年的图线。
参数：colHeatmap
function describing color scheme for the heatmap plot (defaults to YlGnBu from RColorBrewer package).
功能描述颜色的热图积（从RColorBrewer包默认YlGnBu）计划。
参数：showConfidenceIntervals
logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).
逻辑标指示是否要绘制每一个变化点的置信区间（只可用一次分割发生）。
参数：just
character vector specifying the justification of the supplied values to the given coordinates; setting the first entry to "left" indicates that the supplied x-coordinates are the start positions of the probes, change this to "centre" if the x-coordinates are the probe middle positions. Usually the second entry should be "centre" (see grid.rect)
特征向量指定给定的坐标值的理由，第一项设置为“左”表示提供的x坐标起始位置的探针，改变这种“中心”如果x坐标探针中间位置。一般第二项应该是“中心”（见grid.rect）
参数：main
character vector specifying plot title.
特征向量指定小区称号。
参数：makeRasterImage
logical scalar indicating whether to plot the heatmap image by the grid.raster (see grid.raster) or the grid.rect (see grid.rect) function in grid package.The default is to generate raster image, as it can be displayed much faster with a relatively smaller file size.
逻辑标表示是否绘制热图图像grid.raster（见grid.raster）或grid.rect的（grid.rect）在电网package.The默认的功能是生成光栅图像，看到它可以显示一个相对较小的文件大小快得多。
参数：...
additional arguments.
额外的参数。
Details
详情----------Details----------
This function is called by plotAlongChrom if the argument what is set to heatmap. Although this function can be called directly by the user, this is not recommended. The dat list contains the following items:
这种功能被称为plotAlongChrom如果参数what设置为heatmap。虽然这个功能可以由用户直接调用，这是不推荐使用。 dat列表包含下列项目：
x x-coordinates (in bases) along chromosome
xx坐标沿染色体（碱基）
y intensity matrix of probes along chromosome
y沿染色体的探针强度矩阵
flag indicates probe uniqueness in the genome. Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.
flag表明探针在基因组中的唯一性。可能性3：多个完美的比赛，2：有没有PM，但一个或多个比赛，1附近有一个PM和一些基因组中，近比赛：有一个PM和附近没有匹配。
extras (optional) matrix of additional values (such as test-statistics/p-values) to be plotted
extras（可选）附加价值矩阵（如test-statistics/p-values）要绘制
作者（S）----------Author(s)----------
Wolfgang Huber <huber@ebi.ac.uk>
举例----------Examples----------
data(segnf)
data(gffSub)
nmLabel = colnames(segnf$"1.+"@y)
plotAlongChrom(segnf,chr=1,coord=c(35000,50000),what="heatmap",
gff=gffSub,rowNamesHeatmap=nmLabel) ##using raster image[＃使用栅格图像]
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 15:35:37
