writeReport(cellHTS)
writeReport()所属R语言包：cellHTS
Create a directory with HTML pages of linked tables and plots
创建HTML页面的链接表和图目录
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creates a directory with HTML pages of linked tables and plots
创建HTML页面的链接表和图目录
用法----------Usage----------
writeReport(x,
outdir=file.path(getwd(), x$name),
force=FALSE,
plotPlateArgs=FALSE,
imageScreenArgs=NULL,
progressReport = interactive(),
posControls,
negControls)
参数----------Arguments----------
参数：x
a cellHTS object.
cellHTS对象。
参数：outdir
a character of length 1 with the name of a directory where to write the report HTML file and images. If the directory does not exist, it is created. If it exists and is not empty, then the behaviour depends on the value of force.
字符的目录的名称写报告HTML文件和图像的长度1。如果该目录不存在，则创建它。如果它存在，并且不为空，则行为取决于上force值。
参数：force
a logical value, determines the behaviour of the function if outdir exists and is not empty. If force is TRUE, the function overwrites (removes and recreates) outdir, otherwise it casts an error.
一个逻辑值，决定如果outdir存在，并且不为空的函数的行为。 force如果是TRUE，功能覆盖（删除并重新创建）outdir，否则施放的错误。
参数：plotPlateArgs
either a list with parameters for the plate plots of the per plate quality report pages, or a logical scalar with values FALSE or TRUE. If FALSE, the plate plots are omitted, this option is here because the production of the plate plots takes a long time. See details.
无论是板每板质量报告页面图列表参数，或与逻辑标值FALSE或TRUE。如果FALSE，板图被忽略，此选项是这里生产的板图，因为需要较长的时间。查看详情。
参数：imageScreenArgs
a list with parameters for the function imageScreen. See details.
与功能imageScreen参数列表。查看详情。
参数：progressReport
a logical, should a progress report window be displayed?
一个逻辑，应该显示进度报告窗口？
参数：posControls
a list or vector of regular expressions specifying the name of the positive controls. See details.
正则表达式指定的阳性对照的名称列表或向量。查看详情。
参数：negControls
a vector of regular expressions specifying the name of the negative controls. See details.
一个正则表达式的向量指定名称的阴性对照。查看详情。
Details
详情----------Details----------
The following elements are recognized for plotPlateArgs and passed on to plotPlate: sdcol, the color scheme for the standard deviation plate plot, sdrange, the sd range to which the colors are mapped, xcol, the color scheme for the intensity plate plot, xrange, the intensity range to which the colors are mapped. If an element is not specified, default values are used.
以下元素被确认为plotPlateArgsplotPlate：sdcol，标准偏差板图的配色方案，sdrange，SD系列，颜色，并通过对映射，xcol，强度钢板图的配色方案，xrange，强度范围的颜色映射。如果一个元素没有被指定，则使用默认值。
The following elements are recognized for imageScreenArgs and passed on to imageScreen: ar, aspect ratio, zrange, range, map, logical value indicating whether tooltips with the annotation should be added to the plot (default value is FALSE), anno, gene annotation for the image map.
以下要素确认为imageScreenArgs“传递给imageScreen：ar，长宽比，zrange，范围，map，逻辑值，指示是否工具提示注释应该被添加到图（默认值为FALSE），anno影像图，基因注释。
posControls and negControls should be given as a vector of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and stored in x$wellAnno). The length of these vectors should be equal to the number of reporters used in the screen (dim(x$xraw)[4] or to dim(x$xnorm)[4], in case x contains multi-channel data that have been normalized by combining the values from two or more channels). By default, if posControls is not given, "pos" will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in x$wellAnno (see examples). If no controls are available for a given channel, use "" or NA for that channel. For example, posControls = c("", "(?i)^diap$") means that channel 1 has no positive controls, while "diap" is the positive control for channel 2.
posControls和negControls应作为向量的正则表达式指定模式（S）的积极和消极的（S）控制，respectivey板配置文件中提供的名称（和存储x$wellAnno）。这些向量的长度应该等于记者在屏幕上使用的数量（dim(x$xraw)[4]或dim(x$xnorm)[4]，x包含多通道数据相结合，已标准化值由两个或两个以上的渠道）。默认情况下，如果posControls没有给出，“POS”将被视为包含阳性对照井的名字。同样，如果negControls缺少，默认情况下，“南德”将被视为阴性对照用来注释的名称。 posControls和negControls将传递给regexpr在x$wellAnno（见例子）给出了很好的注释模式匹配的内容。如果没有控制对于一个给定的通道，该通道使用""或NA。例如，posControls = c("", "(?i)^diap$")1通道意味着没有阳性对照，而“diap”通道2的阳性对照。
The arguments posControls and negControls are particularly useful in multi-channel data since the controls might be reporter-specific, or after normalizing multi-channel data.
论据posControls和negControls是特别有用的，因为在多通道数据的控制可能是特定的记者，或标准化后多通道数据。
In case of a two-way assay, where two types of "positive" controls are used in the screen ("activators" and "inhibitors"), posControls should be defined as a list with two components (called act and inh), each of which should be vectors of regular expressions of the same length as the current number of reporters (as explained above).
在双向法，在屏幕上使用两种类型的“积极”的控制（“激活”和“抑制剂”），posControls应定义为两部分组成名单（称为act和inh），其中每一个应该作为当前的记者人数（如上所述）的相同长度的正则表达式的向量。
By default, tooltips doing the mapping between the probe annotation and the plate wells are not added to the plate plots and to the overall screen plot. If the cellHTS object x is annotated, the probe annotation is based on the information contained whether in x$geneAnno$GeneSymbol, or x$geneAnno$GeneID, if the former is missing. Otherwise, the mapping simply uses the well identifiers.
默认情况下，提示做探针注释和板井之间的映射不会加入到板图和整体画面图。如果cellHTS对象x是注释，探针注释是基于所载资料是否在x$geneAnno$GeneSymbol或x$geneAnno$GeneID，如果是前者丢失。否则，简单的映射使用以及标识符。
值----------Value----------
The function is called for its side-effect. It returns a character with the full path and name of the report index file, this is an HTML file which can be read by a web browser.
该功能被称为其副作用。它返回一个字符，报告索引文件的完整路径和名称，这是一个HTML文件，可以通过网页浏览器读取。
作者（S）----------Author(s)----------
Ligia Braz <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>, Wolfgang Huber
<a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>
参见----------See Also----------
plotPlate, imageScreen
plotPlate，imageScreen
举例----------Examples----------
data(KcViabSmall)
## pCtrls <- c("pos") [＃pCtrls < - C（“POS”）]
## nCtrls <- c("neg") [＃nCtrls < - C（“负”）]
## or for safety reasons (not a problem for the current well[＃或出于安全的原因（不是一个好当前的问题]
## annotation, however) [＃注释，但是）]
## pCtrls <- c("^pos$") [＃pCtrls < - C（“^ $ POS”）]
## nCtrls <- c("^neg$")[＃nCtrls < - C（“^ NEG $”）]
## writeReport(KcViabSmall, posControls=pCtrls, negControls=nCtrls)[＃writeReport（KcViabSmall，posControls = pCtrls，negControls = nCtrls）]
## same as [＃一样]
## writeReport(KcViabSmall)[＃writeReport（KcViabSmall）]
## Not run: [＃无法运行：]
x <- normalizePlates(KcViabSmall, normalizationMethod="median",zscore="-")
x <- summarizeReplicates(x, summary="min")
writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs=list(zrange=c(-4,4)))
## End(Not run)[＃结束（不运行）]
## to turn on the tooltips in the overall screen image plot:[＃在整个屏幕图像图工具提示：]
## writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs = list(zrange=c(-4,4), map=TRUE))[，，＃writeReport（X，力= TRUE，plotPlateArgs =列表（），imageScreenArgs =列表（zrange = C（-4,4），MAP = 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 2012-2-25 14:22:49
