Plot.subjects(GlobalAncova)
Plot.subjects()所属R语言包：GlobalAncova
Subjects Plot for GlobalAncova
GlobalAncova为主题图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Produces a plot to show the influence of the samples on the test result produced by GlobalAncova.
产生一个图由GlobalAncova产生的测试结果显示样品的影响。
There are three possible ways of using GlobalAncova. Also Plot.subjects can be invoked with these three alternatives.
使用GlobalAncova有三种可能的方式。 Plot.subjects可以调用这三个替代品。
用法----------Usage----------
## S4 method for signature 'matrix,formula,formula,ANY,missing,missing,missing'
Plot.subjects(xx, formula.full, formula.red, model.dat, group,covars = NULL, test.terms,test.genes, Colorgroup = NULL, sort = FALSE, legendpos = "topright", returnValues = FALSE, bar.names, ...)
## S4 method for signature 'matrix,formula,missing,ANY,missing,missing,character'
Plot.subjects(xx, formula.full,formula.red, model.dat, group,covars = NULL, test.terms,test.genes, Colorgroup = NULL, sort = FALSE, legendpos = "topright", returnValues = FALSE, bar.names, ...)
## S4 method for signature 'matrix,missing,missing,missing,ANY,ANY,missing'
Plot.subjects(xx, formula.full, formula.red, model.dat, group,covars = NULL, test.terms,test.genes, Colorgroup = NULL, sort = FALSE, legendpos = "topright", returnValues = FALSE, bar.names, ...)
参数----------Arguments----------
参数：xx
Matrix of gene expression data, where columns correspond to samples and rows to genes. The data should be properly normalized beforehand (and log- or otherwise transformed). Missing values are not allowed. Gene and sample names can be included as the row and column names of xx.
基因表达数据矩阵，列对应的基因样本和行。数据应妥善事先标准化（log或以其他方式转化）。遗漏值是不允许的。基因和样本的名称，可以包含作为xx行和列的名称。
参数：formula.full
Model formula for the full model.
整个模型的模型公式。
参数：formula.red
Model formula for the reduced model (that does not contain the terms of interest.)
减少模型的模型公式（不包含权益的条款。）
参数：model.dat
Data frame that contains all the variable information for each sample.
数据框包含每个样品的所有变量的信息。
参数：group
Vector with the group membership information.
向量组成员信息。
参数：covars
Vector or matrix which contains the covariate information for each sample.
向量或矩阵，其中包含了每个样品的协信息。
参数：test.terms
Character vector that contains names of the terms of interest.
特征向量包含利益的条款的名称。
参数：test.genes
Vector of gene names or gene indices specifying the gene set. If missing, the plot refers to all genes in xx.
向量的基因名称或指定的基因组的基因指标。如果丢失，图是指在xx所有的基因。
参数：Colorgroup
Character variable giving the group that specifies coloring. If the function is called using the argument group then this variable is assumed to be relevant for coloring.
字符变量组，指定着色。如果该功能被称为使用参数group那么这个变量被认为是色素有关。
参数：sort
Should the samples be ordered by colorgroup?
样品应责令colorgroup？
参数：legendpos
Position of the legend (a single keyword from the list '"bottomright"', '"bottom"', '"bottomleft"', '"left"', '"topleft"', '"top"', '"topright"', '"right"' and '"center"').
传说中的位置（从单一关键字名单“bottomright”，“底部”，“”bottomleft“，”左“，”左上“，”顶“ ，“topright”，“权利”和“中心”）
参数：returnValues
Shall bar heights (subject-wise reduction in sum of squares) be returned?
条形的高度应（明智主题平方和减少）回来了吗？
参数：bar.names
Vector of bar labels. If missing, column names of xx are taken.
矢量栏标签。如果缺少，的xx列名采取。
参数：...
Graphical parameters for specifying colors, titles etc.
指定的颜色，标题等图形参数
方法----------Methods----------
xx = "matrix", formula.full = "formula", formula.red = "formula", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "missing" In this method, besides the expression matrix xx, model formulas for the full and reduced model and a data frame model.dat specifying corresponding model terms have to be given. Terms that are included in the full but not in the reduced model are those whose association with differential expression will be tested. The arguments group, covars and test.terms are '"missing"'
XX =“矩阵”，formula.full =“公式”，formula.red =“的公式”，model.dat =“任何”，组=“失踪”，covars =“失踪”，测试。条件=“失踪”在这种方法中，除了表达矩阵，xx，充分和减少模型和数据框model.dat指定相应的模型计算，必须给模型公式。在全包括，但不是在减少模型的条款，其差异表达的关系将受到考验。的论点group，covars和test.terms是“失踪”
xx = "matrix", formula.full = "formula", formula.red = "missing", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "character" In this method, besides the expression matrix xx, a model formula for the full model and a data frame model.dat specifying corresponding model terms are required. The character argument test.terms names the terms of interest whose association with differential expression will be tested. The arguments formula.red, group and covars are '"missing"'
XX =“矩阵”，formula.full =“公式”，formula.red =“失踪”，model.dat =“任何”，组=“失踪”，covars =“失踪”，测试。条款=“字符”，在此方法中，除了表达矩阵xx，一个完整的模型和数据框的模型公式model.dat指定相应的模型计算需要。字符参数test.terms命名权益的条款，其差异表达的关系将受到考验。的论点formula.red，group和covars是“失踪”
xx = "matrix", formula.full = "missing", formula.red = "missing", model.dat = "missing", group = "ANY", covars = "ANY", test.terms = "missing" Besides the expression matrix xx a clinical variable group is required. Covariate adjustment is possible via the argument covars but more complex models have to be specified with the methods described above. This method emulates the function call in the first version of the package. The arguments formula.full, formula.red, model.dat and
XX =“矩阵”，formula.full =“失踪”，formula.red =“失踪”，model.dat =“失踪”，组=的“ANY”，covars =“任何”，测试。 =“失踪”除了表达矩阵xx临床变量group是必需的。协变量调整是可能通过参数covars但更复杂的模型必须与上面描述的方法指定。这种方法模拟包的第一个版本的功能调用。参数formula.full，formula.red，model.dat“
注意----------Note----------
This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.
这项工作是NGFN项目01的GR 0459，BMBF的，德国的支持。
作者（S）----------Author(s)----------
Reinhard Meister <a href="mailto:meister@tfh-berlin.de">meister@tfh-berlin.de</a><br>
Ulrich Mansmann <a href="mailto:mansmann@ibe.med.uni-muenchen.de">mansmann@ibe.med.uni-muenchen.de</a><br>
Manuela Hummel <a href="mailto:hummel@ibe.med.uni-muenchen.de">hummel@ibe.med.uni-muenchen.de</a>
参见----------See Also----------
GlobalAncova, Plot.genes, Plot.sequential
GlobalAncova，Plot.genes，Plot.sequential
举例----------Examples----------
data(vantVeer)
data(phenodata)
data(pathways)
Plot.subjects(xx = vantVeer, formula.full = ~metastases + ERstatus, formula.red = ~ERstatus, model.dat = phenodata, test.genes = pathways[[3]], colorgroup = "metastases")
Plot.subjects(xx = vantVeer, formula.full = ~metastases + ERstatus, test.terms = "metastases", model.dat = phenodata, test.genes = pathways[[3]], colorgroup = "metastases")
Plot.subjects(xx = vantVeer, group = phenodata$metastases, covars = phenodata$ERstatus, test.genes = pathways[[3]])
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 20:42:03
