hopach2tree(hopach)
hopach2tree()所属R语言包：hopach
function to write MapleTree files for viewing hopach hierarchical clustering results
函数写枫树查看hopach分层聚类结果的文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The MapleTree software (http://mapletree.sourceforge.net/) is an open source, cross-platform, visualization tool to graphically browse results of cluster analyses. The hopach2tree function takes a data matrix, plus corresponding hopach clustering output for genes and/or arrays, and writes the (.cdt, .gtr, and .atr) files needed to view these hierarchical clustering results in MapleTree. The function makeTree is called internally by hopach2tree.
丰树软件（http://mapletree.sourceforge.net/）的是一个开源，跨平台，可视化工具，以图形方式浏览聚类分析的结果。函数需要hopach2tree数据矩阵，加上相应的hopach聚类的基因和/或阵列输出，并写入（。CDT。GTR。ATR）的文件，需要查看这些层次聚类结果在丰树。函数makeTree内部被称为hopach2tree。
用法----------Usage----------
hopach2tree(data, file = "HOPACH", hopach.genes = NULL, hopach.arrays = NULL,
dist.genes = NULL, dist.arrays = NULL, d.genes = "cosangle",
d.arrays = "euclid", gene.wts = NULL, array.wts = NULL, gene.names = NULL)
makeTree(labels, ord, medoids, dist, side = "GENE")
参数----------Arguments----------
参数：data
data matrix, data frame or exprSet of gene expression measurements. Each column corresponds to an array, and each row corresponds to a gene. All values must be numeric. Missing values are ignored.
数据矩阵，基因表达测量的数据框或exprSet。每列对应一个数组，每一行对应一个基因。所有的值必须是数字。遗漏值将被忽略。
参数：file
name for the output files (the extensions .cdt, .gtr and .atr will be added).
输出文件（扩展名。CDT，将增加。GTR。ATR）。
参数：hopach.genes
output of the hopach function applied to genes (rows of data. If only arrays are clustered, hopach.genes can be NULL. There must be at least K=2 levels in the hopach final tree (ie: hopach.genes$final$labels greater than 1 digit) for a gtr file to be generated.
hopach应用功能基因（data。hopach.genes如果只有阵列聚类，可以为NULL。必须有至少k = 2水平在最后hopach树（即行输出hopach.genes美元最终为标签大于1位为GTR文件）来生成。
参数：hopach.arrays
optional output of the hopach function applied to arrays (columns of data. There must be at least K=2 levels in the hopach final tree (ie: hopach.arrays$final$labels greater than 1 digit) for an atr file to be generated.
可选的输出hopach功能应用到阵列（列必须有至少为k = 2水平在最后hopach树（即：data。hopach.arrays美元最终为标签大于1位）ATR文件要生成。
参数：dist.genes
matrix of pair wise distances between all genes. All values must be numeric, and missing values are not allowed. If NULL, this matrix is computed using the metric specified by d.genes. Only needed if genes are clustered (hopach.genes!=NULL).
矩阵成对所有基因之间的距离。所有的值必须是数字，不允许遗漏值。如果为NULL，这使用d.genes指定的度量矩阵计算。只需要基因聚集（hopach.genes！=空）。
参数：dist.arrays
matrix of pair wise distances between all arrays. All values must be numeric, and missing values are not allowed. If NULL, this matrix is computed using the metric specified by d.arrays. Only needed if arrays are clustered (hopach.arrays!=NULL).
矩阵成对所有阵列之间的距离。所有的值必须是数字，不允许遗漏值。如果为NULL，这使用d.arrays指定的度量矩阵计算。只需要阵列聚类（hopach.arrays！=空）。
参数：d.genes
character string specifying the metric to be used for calculating dissimilarities between genes. The currently available options are "cosangle" (cosine angle or uncentered correlation distance), "abscosangle" (absolute cosine angle or absolute uncentered correlation distance), "euclid" (Euclidean distance), "abseuclid" (absolute Euclidean distance), "cor" (correlation distance), and "abscor" (absolute correlation distance). Advanced users can write their own distance functions and add these to the functions distancematrix() and distancevector().
字符串指定的度量用于计算基因之间的异同。目前可用的选项是“cosangle”（余弦角或者非中心的相关距离），的“abscosangle”（绝对余弦角度或绝对非中心相关距离），“欧几里得”（欧氏距离），的“abseuclid”（绝对欧氏距离），“心病”（相关距离），和“abscor”（绝对相关距离）。高级用户可以编写自己的距离函数，并添加这些功能distancematrix()和distancevector()。
参数：d.arrays
character string specifying the metric to be used for calculating dissimilarities between arrays.
字符串指定的度量用于计算阵列之间的异同。
参数：gene.wts
an optional vector of numeric weights for the genes.
数字基因重可选向量。
参数：array.wts
an optional vector of numeric weights for the arrays.
可选的数字阵列权重向量。
参数：gene.names
optional vector of names or annotations for the genes, which can be different from the row names of data.
可选名称或注释的基因向量，它可以是data行名称不同。
参数：labels
final cluster labels from a hopach object.
从hopach对象的最终簇标签。
参数：ord
final ordering from a hopach object.
最后订购从hopach对象。
参数：medoids
final medoids matrix from a hopach object.
最后中心点矩阵从hopach对象。
参数：dist
gene or array distance matrix.
基因或阵列的距离矩阵。
参数：side
character string specifying if the tree is for genes ("GENE", default) or arrays ("ARRY").
字符串指定，如果树的基因（“基因”，默认）或阵列（“哈利”）。
值----------Value----------
The function hopach2tree has no value. It writes up to three text files to the current working directory. A .cdt file is always produced. This file can be used to visualize the data matrix as a heat map in MapleTree or other viewers such as TreeView (http://rana.lbl.gov/EisenSoftware.htm), jtreeview (http://sourceforge.net/projects/jtreeview/), and GeneXPress (http://genexpress.stanford.edu/). When hopach.genes!=NULL, a .gtr is produced, and gene clustering results can be viewed, including ordering the genes in the heat map according to the final level of the hopach tree and drawing the dendogram for hierarchical gene clustering. Similarly, when hopach.arrays!=NULL, an .atr file is produced and array clustering results can be viewed.
功能hopach2tree有没有价值。它写了三个文本文件到当前工作目录。总是产生。CDT文件。这个文件可以用于可视化数据矩阵作为一个在丰树或其他观众的TreeView（http://rana.lbl.gov/EisenSoftware.htm），jtreeview（http://sourceforge.net/projects/如热图jtreeview /），GeneXPress（http://genexpress.stanford.edu/）。当hopach.genes！= NULL。GTR产生，基因的聚类结果可以查看，包括在热图订购的根据hopach树的最后一级的基因和借鉴的dendogram分层基因聚类。同样，当hopach.arrays！= NULL。ATR文件制作和数组聚类结果可以被看作。
The function makeTree is called internally by hopach2tree to make the objects needed to write the MapleTree files for a gene and/or array HOAPCH clustering result.
功能makeTree内部被称为hopach2tree写的基因和/或阵列HOAPCH聚类结果的枫树文件所需的对象。
警告----------Warning ----------
Operating systems use different end of line characters. These characters can cause errors in MapleTree when files generated on one OS are visualized on another OS. Hence, hopach2tree should be run on the same OS as MapleTree whenever possible.
操作系统使用不同的终端行的字符。这些字符可能会导致在丰树的错误，当一个操作系统上生成的文件是在另一个操作系统的可视化。因此，hopach2tree应为丰树相同的操作系统尽可能上运行。
注意----------Note----------
Thank you to Lisa Simirenko <lsimirenko@lbl.gov> for providing HOPACH views in MapleTree, and to Karen Vranizan <vranizan@uclink.berkeley.edu> for her input.
谢谢丽莎Simirenko <lsimirenko@lbl.gov>，提供丰树HOPACH的意见，并卡伦Vranizan <vranizan@uclink.berkeley.edu>的她输入。
The MapleTree software can be downloaded from: http://sourceforge.net/projects/mapletree/
枫树软件可以下载：http://sourceforge.net/projects/mapletree/
作者（S）----------Author(s)----------
Katherine S. Pollard <kpollard@gladstone.ucsf.edu>
参考文献----------References----------
参见----------See Also----------
hopach, boothopach, bootmedoids, boot2fuzzy
hopach，boothopach，bootmedoids，boot2fuzzy
举例----------Examples----------
#25 variables from two groups with 3 observations per variable[25两组每3个变量观测变量]
mydata<-rbind(cbind(rnorm(10,0,0.5),rnorm(10,0,0.5),rnorm(10,0,0.5)),cbind(rnorm(15,5,0.5),rnorm(15,5,0.5),rnorm(15,5,0.5)))
dimnames(mydata)<-list(paste("Var",1:25,sep=""),paste("Exp",1:3,sep=""))
mydist<-distancematrix(mydata,d="cosangle") #compute the distance matrix.[计算距离矩阵。]
#clusters and final tree[聚类和最终树]
clustresult<-hopach(mydata,dmat=mydist)
#write MapleTree files[写枫树文件]
hopach2tree(mydata,hopach.genes=clustresult,dist.genes=mydist)
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 21:46:36
