buildNet(GeneAnswers)
buildNet()所属R语言包：GeneAnswers
build and display a network for given IDs and interaction Matrix
建立并显示一个给定的ID和互动矩阵网络
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A function to build and display a network for given IDs and interaction Matrix with specified filtered IDs.
函数建立并显示一个网络ID和互动矩阵与指定过滤的ID。
用法----------Usage----------
buildNet(graphIDs, idType=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction', 'Customized'), edgeM=NULL, layers=1, filterGraphIDs=NULL, filterLayer=0,
annLib=c('org.Hs.eg.db', 'org.Mm.eg.db', 'org.Rn.eg.db', 'org.Dm.eg.db', 'customized'), output=c('interactive', 'fixed'), netMode=c('layer', 'connection'),
vertexSize = NULL, edgeColor = NULL, colorMap=NULL, zeroColorIndex=NULL, matchMode=c('absolute', 'relative'), label=TRUE, steric=FALSE,
directed=FALSE, direction=c('up', 'down', 'both'), showModeForNodes=c('nodes', 'filters'), verbose=TRUE, readable=TRUE, labelSize=1, labelColor='#666666', ...)
参数----------Arguments----------
参数：graphIDs
a character vector for given IDs
一个给定的ID的特征向量
参数：idType
type of IDs, could be one of 'GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction' and 'Customized'
ID的类型，可能是GO，GO.BP，GO.CC，GO.MF，GeneInteraction“和”定制“
参数：edgeM
a 2-column Matrix representing a network
2列的矩阵网络
参数：layers
an integer, specify how many layers will be retrieved.
一个整数，指定将检索多少层。
参数：filterGraphIDs
a chacater vector for filtered IDs or a 2- or 3-column matrix for extra values.
为筛选ID或2 chacater向量 - 或3列矩阵的附加价值。
参数：filterLayer
an integer, specify where filterGraphIDs are applied.
一个整数，指定应用filterGraphIDs的。
参数：annLib
type for annotation library, 'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Rn.eg.db', 'org.Dm.eg.db'and 'customized'. For 'customized', edgeM is necessary
类型注释库org.Hs.eg.db“，”org.Mm.eg.db，org.Rn.eg.db，org.Dm.eg.db“和”定制“。对于“定制”，edgeM是必要的
参数：output
type to specify output figure types
键入指定输出数字类型
参数：netMode
type to show network, see details
键入显示网络，查看详细信息
参数：vertexSize
an integer, the size of vertices in the network, default is NULL
一个整数，在网络中的顶点的大小，默认值为NULL
参数：edgeColor
a R compatible color type, the color of edges in the network, default is NULL
一个R兼容的彩色类型，在网络边缘的颜色，默认值为NULL
参数：colorMap
a R compatible color character vector, or NULL by embedded color scheme.
一个R兼容的彩色特征向量，或NULL嵌入式配色方案。
参数：zeroColorIndex
index of color corresponding to zero, see details
对应于零的显色指数，查看详细信息
参数：matchMode
the mode of values matching colors, valid only if inputValue is not NULL, see details
值配色模式，有效的，只有当inputValue不为NULL，查看详细信息
参数：label
logic, specify whether put labels for non-given nodes in the network.
逻辑，指定是否把网络中的非定节点的标签。
参数：steric
logic, specify whether show 3D network. Because of igraph limited support for 3D, this function is just for fun!
逻辑，指定是否显示三维网络。因为IGRAPH三维有限的支持，此功能只是为了好玩！
参数：directed
logic, the network is a directed or not
逻辑，网络是一个定向或不
参数：direction
search direction, it could be 'up', 'down' and 'both'. Valid for directed network only.
搜索方向，它可能是“”，“下”和“都”。仅向网络有效。
参数：showModeForNodes
type, the show mode for nodes on the network, only valid if filterGraphIDs is not NULL, see details
类型，网络上的节点，只有filterGraphIDs有效的显示模式是不是NULL，查看详细信息
参数：verbose
logic, specify to show information or not.
逻辑，指定或不显示信息。
参数：readable
logic, specify whether show IDs or Terms/Names for nodes
逻辑，指定是否显示ID或条款/节点的名称
参数：labelSize
an integer, the size of label for nodes
一个整数，节点标签的大小
参数：labelColor
an R compatible color, default is #666666
一个R兼容的颜色，默认为＃666666
参数：...
other parameters used by 'getCategoryTerms'
使用getCategoryTerms“的其他参数
Details
详情----------Details----------
Currently, if idType is 'GO', 'GO.BP', 'GO.CC' or 'GO.MF', edgeM will be ignore.
目前，edgeM，如果idType被GO，GO.BP，GO.CC“或”GO.MF“，将被忽略。
edgeM is a 2-column matrix. For directional connection, the direction is from column 1 elements to column 2 elements. For non-directional connection, each connection should be reversely presented twice, one is from column 1 element to column 2 element, while another is from column 2 element to column 1 element. In other words, non-directional connection is considered as two reverse directional connections.
edgeM是一个2列的矩阵。定向连接，方向是从1列2列元素的元素。对于非定向的连接，每个连接反应提出两次，一个是从1元列第2列元素，而另一个是从第2列元素1列元素。换句话说，非定向的连接被视为两个相反方向的连接。
filterGraphIDs are applied only at the filterLayer and more outer layers. This means the nodes between the filterLayer layer and the most external layer belong to the filterGraphIDs. The nodes between given graphIDs and the (filterLayer-1) layer are or are not from filterGraphIDs, but those nodes not in filterGraphIDs should be able to be finally connected by given graphIDs and filterGraphIDs.
filterGraphIDs只适用于在filterLayer和更外层。这意味着节点之间的filterLayer层和最外层属于该filterGraphIDs的。在节点之间给予graphIDs（filterLayer-1）层或从filterGraphIDs的，但应该能够给予graphIDs和filterGraphIDs最终连接这些节点不filterGraphIDs。
There are two type of color matching methods. 'absolute' means, given zeroColorIndex that is color index in the colorMap for value 0, any value more than 0 will be matched to color between zeroColorIndex and the last one in colorMap based on the ratio of the value tothe maximum of the inputValue, while the value less than 0 will be matched to color between the first color in colorMap and zeroColorIndex, also based on the ratio of the value to the minimum of the inputValue.
配色的方法有两种类型。 “绝对”的手段，给予zeroColorIndex是在colormap色指数为0值，任何价值超过0将匹配之间zeroColorIndex和基于价值带来更多更棒最大的inputValue比在colormap中的最后一个颜色，而小于0的值将被匹配颜色之间的颜色也到最低的inputValue的价值的比例为基础，在Colormap和zeroColorIndex的第一。
showModeForNodes stands for, if the filterGraphIDs is not NULL, some or all of filterGraphIDs could be nodes for given IDs multiple search. If it is set to 'nodes', it means only the values of nodes in the display network will be used to match color by matchMode. For 'filters', it means the values of all filter nodes will be used to match color. If values for color of nodes in the network are not large, while the maximum of color of filter nodes is large, it is recommended to set to 'nodes', or it is difficult to see difference for the nodes. For comparing two networks, for example, one is up-search and another is down-search for the same IDs, it is better to set to 'absolute' for easy comparisons.
showModeForNodes代表的filterGraphIDs，如果不为NULL，可以部分或全部的filterGraphIDs给定ID的多个搜索节点。如果它被设置为“节点”，这意味着只显示网络中的节点的值将用来匹配matchMode颜色的。对于“过滤器”，它意味着所有过滤器节点的值将被用来匹配的颜色。如果在网络节点的颜色值并不大，而最大的过滤器节点的颜色是很大的，它建议设置“节点”，或很难看到节点的差异。比较两个网络，例如，一个是搜索，另一个是为相同ID的搜索，最好是设置为“绝对”，便于比较。
There are two types of output figures. "Fixed" means a network will be drawn on a regular R canvas, while "interactive" will generate a tck/tk canvas. Users can adjust nodes on it by mouse.
有两种类型的输出数字。 “固定”是指将网络上绘制定期ŕ画布，而“互动”，将产生一个TCK / TK的画布。用户可以通过鼠标调整它的节点。
If the filterGraphIDs is a ID vector. The filterGraphIDs nodes will be black, others will be white. If filterGraphIDs is a 2- or 3-column matrix, the 1st column is filter IDs and 2nd column is for color of nodes. If the 3rd column is available, it is for size of nodes.
如果的filterGraphIDs是一个ID向量。的filterGraphIDs节点将是黑色的，别人也会是白色的。如果的filterGraphIDs是一个2 - 3列的矩阵，第一列是过滤器的ID和节点的颜色是第二列。如果第三列是可用的，它是节点的大小。
There are two types of netMode. 'layer' means size of nodes will be smaller and smaller for more and more external layers. And also color of edges change for different layers. 'connection' mode just distinguish direct or indirect connection. The size of the given IDs the largest. However, if filterGraphIDs is a 3-column matrix, the size of nodes will be determined by the 3rd column of filterGraphIDs.
有两个netMode。 “层”是指节点的规模将是较小的和越来越多的外部层。并且边的颜色改变为不同的层次。 “连接”模式只是区分直接或间接连接。给定ID的最大规模。然而，，如果filterGraphIDs是一个3列的矩阵，节点的大小将取决于第三列的filterGraphIDs。
The graphIDs nodes are yellow circled solid dots. Color depends on colorMap and filterGraphIDs 2nd column. If no value available, all given graphIDs filterGraphIDs nodes are black, others are white.
节点的graphIDs黄色圆圈实心圆点。颜色取决于Colormap和filterGraphIDs第二列的。如果没有任何价值，所有graphIDs filterGraphIDs节点都是黑色的，其他都是白色的。
值----------Value----------
invisibly return a list containing elements to represent a network.
无形返回一个列表，其中包含的元素代表一个网络。
作者（S）----------Author(s)----------
Gang Feng, Pan Du and Simon Lin
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
require(GeneAnswers)
example(GeneAnswers)
filterM <- cbind(rownames(getEnrichmentInfo(x)), -log2(getEnrichmentInfo(x)[,7]), getEnrichmentInfo(x)[,1])
## Not run: buildNet(rownames(getEnrichmentInfo(x))[6:9], layers=5, filterGraphIDs=filterM, filterLayer=3, directed=TRUE, output='fixed')[＃无法运行：buildNet（rownames（getEnrichmentInfo（X））[6:9]，层= 5，filterGraphIDs = filterM，filterLayer = 3，定向= TRUE，输出=固定）]
## Not run: buildNet(rownames(getEnrichmentInfo(x))[242:244], layers=2, filterGraphIDs=filterM, filterLayer=1, directed=TRUE, output='fixed', netMode='connection', direction='down')[＃无法运行：buildNet（rownames（getEnrichmentInfo（X））[242:244]，图层= 2，filterGraphIDs = filterM，filterLayer = 1，定向= TRUE，输出=固定，netMode =连接，方向=下“）]
## Not run: buildNet(rownames(getEnrichmentInfo(x))[6:9], layers=3, filterGraphIDs=filterM[,1:2], filterLayer=3, directed=TRUE, output='fixed', netMode='connection')[＃无法运行：buildNet（rownames（getEnrichmentInfo（X））[6:9]，层= 3，filterGraphIDs = filterM [1:2]，filterLayer = 3，定向= TRUE，输出=固定，netMode =连接“）]
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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 18:35:56
