termGraphs(GOstats)
termGraphs()所属R语言包：GOstats
Extraction and Plotting of GO Terms from a GOHyperGResult Object
提取和绘图的开始从GOHyperGResult对象条款
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions extract and plot graph instances representing the relationships among GO terms tested using hyperGTest.
这些功能提取物和图graphGO术语之间的关系的情况下测试使用hyperGTest。
用法----------Usage----------
termGraphs(r, id = NULL, pvalue = NULL, use.terms = TRUE)
inducedTermGraph(r, id, children = TRUE, parents = TRUE)
plotGOTermGraph(g, r = NULL, add.counts = TRUE, max.nchar = 20,
node.colors=c(sig="lightgray", not="white"),
node.shape="plaintext", ...)
参数----------Arguments----------
参数：r
A GOHyperGResult object as returned by hyperGTest when given a GOHyperGParams object as input.
一个GOHyperGResult对象时返回hyperGTestGOHyperGParams对象作为输入。
参数：id
A character vector of category IDs that specifies which terms should be included in the graph.
一个类别ID指定的条款应包括在图的特征向量。
参数：pvalue
Numeric p-value cutoff to use for selecting category terms to include. Will be ignored if id is present.
数字p值截止到选择类别方面，包括使用。 id如果存在将被忽略。
参数：use.terms
Logical value indicating whether a "term" node attribute should be added to the returned graph providing the more descriptive, but possibly much longer, GO Terms.
逻辑值，指明"term"节点属性是否应该被添加到返回的图提供了更多的描述，但也可能更长，去条款。
参数：children
A logical value indicating whether to include direct child terms of the terms specified by id.
一个逻辑值，指示是否由id指定的条款包括直接子项。
参数：parents
A logical value indicating whether to include direct parent terms of the terms specified by id.
一个逻辑值，指示是否由id指定的条款包括直接父条款。
参数：g
A graph object as returned by inducedTermGraph or termGraphs.
一个graph对象inducedTermGraph或termGraphs返回。
参数：add.counts
A logical value indicating whether category size counts should be added to the node labels when plotting.
一个逻辑值，表明品类规模计数是否应该被添加到节点标签打印时。
参数：max.nchar
The maximum character length for node labels in the plot.
最大字符长度为节点标签中的图。
参数：node.colors
A named character vector of length two with compoents sig and not, giving color names for the significant and non-significant nodes, respectively.
一个命名的特征向量长度与compoents中sig和not，对重大和非重大节点，分别给予的颜色名称。
参数：node.shape
This argument controls the shape of the plotted nodes and must take on a value allowed by Rgraphviz.
此参数控制绘制节点的形状，必须采取由Rgraphviz允许值。
参数：...
For plotGOTermGraph, extra arguments are passed to the plot function.
plotGOTermGraph，额外的参数传递给plot功能。
Details
详情----------Details----------
termGraphs returns a list of graph objects each representing one of the connected components of the subgraph of the GO ontology induced by selecting the specified GO IDs (if id is present) or by selecting the GO IDs that have a p-value less that pvalue. If use.terms is TRUE the GO IDs will be translated into GO Term names and attached to the nodes as node attributes (see nodeData). Edges in the graphs go from child (more specific) to parent (less
termGraphs返回的列表graph每个对象代表一个子选择指定的好ID（id如果存在），或选择有去的ID引起的GO本体的连接组件p值少pvalue。如果use.terms是TRUE好标识将被翻译进入术语的名称和连接节点的属性节点（见nodeData）。在图形的边缘去的孩子（更具体）父（少
inducedTermGraph returns a graph object representing the GO graph induced by the terms specified by id. The children and parent arguments control whether direct children and/or direct parents of the terms specified by id are added to the graph (at least one of the two must be
inducedTermGraph返回graph对象代表GO图由id指定的条款引起。 children和parent参数控制直接子女及/直接的父母或指定id的条件是否被添加到图（至少两个必须
plotGOTermGraph Create a plot using Rgraphviz of a graph object as returned by either termGraphs or inducedTermGraph. If a GOHyperGResult object is provided, then the nodes will be colored according to significance (based on the result object's pvalueCutoff) and counts will be added to show the size of the categories.
plotGOTermGraph创建一个图使用Rgraphviz的graph对象要么termGraphs或inducedTermGraph返回。如果GOHyperGResult对象提供，那么节点将进行着色根据意义（基于结果对象的pvalueCutoff）和计数将被添加到显示类别的大小。
作者（S）----------Author(s)----------
Seth Falcon
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 20:56:19
