plotOntologyGraph(GeneAnswers)
plotOntologyGraph()所属R语言包：GeneAnswers
plot the ontology graph
绘制本体图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
plot the ontology graph in graphNEL class, the color of ontology is based on the enrichment p.value
graphNEL类本体，本体的颜色图绘制的基础上浓缩p.value
用法----------Usage----------
plotOntologyGraph(onto.pValue, relatedOntoID, onto.graph, bestOntoID = NULL, onto.graph.closure = NULL, rootID = "DOID:4", ID2Name = NULL, p.value.th = 0.01, fillColor = "white", colorLevel = seq(2, 20, by = 2), relative.color = TRUE, fontsize = 15, colorMap = colorRampPalette(c("white", "red"))(length(colorLevel) + 1), selectionMethod = c("simple", "bestOnly", "all"), omitNode = TRUE, saveImageName = NULL)
参数----------Arguments----------
参数：onto.pValue
a vector ontology p.values, whose names are corresponding ontology IDs
一个向量的本体p.values，其名称是对应的本体标识
参数：relatedOntoID
a vector of related ontology IDs, which will be highlighted.
的相关本体标识的向量，将突出。
参数：onto.graph
an ontology graph in graphNEL class, which keeps the graph of the entire ontology DAG. Each node of it is an ontology ID
graphNEL类本体图，这使整个本体的DAG图。它的每个节点是一个本体ID
参数：bestOntoID
the ontology ID which has most significant p-value
其中最显着的p值本体ID
参数：onto.graph.closure
a flatten ontology graph in graphNEL class, whose edges represent offspring relationships.
1压扁graphNEL类，其边代表后代关系的本体图。
参数：rootID
the root ontology ID in the ontology graph
在本体图根本体ID
参数：ID2Name
a named vector of ontology IDs to ontology terms mapping
本体术语映射的本体标识的命名向量
参数：p.value.th
enrichment p.value threshold to claim as significant
富集p.value阈值要求为显着
参数：fillColor
the default fill color of the ontology nodes
本体节点的默认填充颜色
参数：colorLevel
the level of colors to show the significant enriched ontology terms.
颜色的水平，显示出显着的丰富的本体条款。
参数：relative.color
determine whether the most significant enriched node has the deepest color.
确定最显着的丰富的节点是否有最深的颜色。
参数：fontsize
the font size of ontology terms
本体论方面的字体大小
参数：colorMap
the color map to show the significant enriched ontology terms
显示出显着的丰富的本体论方面的彩色图
参数：selectionMethod
the method to select ontology nodes included in the plot graph
积图中包含的本体节点的方法来选择
参数：omitNode
whether to omit the intermediate insignificant ontology terms between the significant terms and terms with direct gene mapping
是否省略中间微不足道的本体论方面之间的重要术语和直接的基因图谱
参数：saveImageName
the name of image to be save. If it is NULL, then the image will not be saved.
图像被保存的名称。如果它是NULL，那么将不会被保存的图像。
值----------Value----------
Invisibly return a list, which include following elements:
无形返回一个列表，其中包括下列要素：
参数：graph
a graphNEL object includes the ontology subgraph to plot
1 graphNEL对象包括本体子图绘制
参数：layoutAttrs
layoutAttrs used by the Rgraphviz function layoutGraph
的Rgraphviz功能layoutGraph layoutAttrs
参数：layoutNodeAttrs
layoutNodeAttrs used by the Rgraphviz function layoutGraph
的Rgraphviz功能layoutGraph layoutNodeAttrs
参数：layoutEdgeAttrs
layoutEdgeAttrs used by the Rgraphviz function layoutGraph
的Rgraphviz功能layoutGraph layoutEdgeAttrs
参数：nodeRenderAttrs
nodeRenderAttrs used by the graph function nodeRenderInfo
使用图形功能nodeRenderInfo nodeRenderAttrs
参数：edgeRenderAttrs
edgeRenderAttrs used by the graph function edgeRenderInfo
使用图形功能edgeRenderInfo edgeRenderAttrs
These invisibly return information can be used as the input of function plotGraph.
这些无形回报的信息，可以作为输入的功能plotGraph。
作者（S）----------Author(s)----------
Pan DU
参见----------See Also----------
See Also plotGraph and plotGeneFunSummary
plotGraph和plotGeneFunSummary
举例----------Examples----------
data(DO)
geneSummary <- geneFunSummarize('4267', gene2DO.map, DO.graph.closure.gene)[[1]]
pValue <- sapply(geneSummary$sigOntoInfo, function(x) x$pValue)
plotOntologyGraph(pValue, geneSummary$allEvidence, DO.graph.gene, onto.graph.closure=DO.graph.closure.gene, ID2Name=DO.terms, p.value.th=0.001)
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 18:41:45
