R语言 hopach包 bootplot()函数中文帮助文档(中英文对照)

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bootplot(hopach)
bootplot()所属R语言包：hopach

                                        function to make a barplot of bootstrap estimated cluster membership probabilities
                                         功能，使的引导barplot的估计聚类成员概率

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

After clustering, the boothopach or bootmedoids function can be used to estimated the membership of each element being clustered in each of the identified clusters (fuzzy clustering). The proportion of bootstrap resampled data sets in which each element is assigned to each cluster is called the "reappearance proportion" for the element and that cluster. This function plots these proportions in a colored barplot.
聚类后，boothopach或bootmedoids函数可以用来估计聚集在每个所确定的聚类（模糊聚类）每个元素的成员。引导重采样数据套，其中每个元素被分配到每个聚类的比例被称为“再现比例”的元素和该聚类。此功能在一个彩色barplot这些比例的图。


用法----------Usage----------


bootplot(bootobj, hopachobj, ord = "bootp", main = NULL, labels = NULL,
showclusters = TRUE, ...)



参数----------Arguments----------

参数：bootobj
output of boothopach or bootmedoids applied to the genes - a matrix of bootstrap estimated cluster membership probabilities, with a row for each row in data and a column for each cluster.
boothopach或bootmedoids应用于基因 - data和每个聚类列的每一行的行引导估计聚类成员概率矩阵，输出。


参数：hopachobj
output of the hopach function. If bootobj was generated using bootmedoids (i.e. hopach was not run), then the bootplot function can be used by creating a hopachobj which is a list with at least the following two components: hopachobj$clustering$sizes (number of elements in each cluster - length should be ncol(bootobj) and hopachobj$clustering$order (an ordering of the elements so that elements in the same cluster appear next to each other and elements may also be ordered within cluster). By changing the value of hopachobj$clustering$order, the order of the elements in the barplot can be altered.
hopach函数的输出。如果bootobj使用bootmedoids（即hopach无法运行），然后bootplot函数可以被用来创建一个hopachobj这是一个列表至少在以下两部分组成：hopachobj$clustering$sizes（每个簇中的元素 - 长度应该是ncol(bootobj)和hopachobj$clustering$order（订购的元素，所以在同一个聚类，要素旁边出现也可以责令对方和要素聚类内）改变hopachobj$clustering$order值。，在barplot元素的顺序可以改变。


参数：ord
character string indicating how to order the elements (rows) in the barplot. If ord="none", then the elements are plotted in the same order as in bootobj, i.e. the same order as the original data matrix. If ord="final", the ordering of elements in the final level of the hopach hierarchical tree is used. If ord="cluster", the ordering from the level of the hopach tree corresponding to the main clusters is used. If ord="bootp", the elements are ordered first by main cluster and then by bootstrap reappearance proportion within cluster, so that elements with the highest membership in the cluster appear at the bottom. In the last three cases, the elements from each cluster will be contiguous. If ord="final", then the medoid element will appear in the middle of each cluster. If ord="clust", the ordering depends on the value of the ord argument passed to the hopach function.  For example, when ord="own" in hopach, the elements are ordered within cluster based on distance to the medoid, so that the medoid appears first (at the bottom) in the cluster.
字符串指示如何在barplot订购元素（行）。如果ORD =“无”，然后绘制在同一顺序的元素在bootobj顺序相同，即作为原始数据矩阵。如果条例“最终”，最后一级hopach分层树中的元素顺序。如果ORD =“聚类”，hopach树对应的主要聚类水平的顺序使用。如果ORD =“BOOTP”，这些元素是有序的，首先由主聚类，然后由引导聚类内再现比例，使聚类中的成员最高的元素出现在底部。在过去的三宗情况中，从每个聚类的元素将是连续的。如果ORD =“最后”，然后medoid元素将出现在每个聚类中。如果ORD =“clust”，顺序取决于ord参数值传递给hopach函数。例如，当ORD =“自己的”hopach的元素是有序的基于距离的medoid聚类内，这样的medoid首先出现在聚类（底部）。


参数：main
character string to be used as the main title
字符串作为主标题使用


参数：labels
a vector of labels for the elements being clustered to be used on the axes. If the number of elements is lager than 50, the labels are not shown.
一个正在聚集轴元素的标签的向量。如果元素的数目超过50啤酒，标签不显示。


参数：showclusters
indicator of whether or not to show the cluster boundaries on the plot. If show.clusters=TRUE, solid lines are drawn at the edges of the clusters.
是否在图上显示的聚类边界的指标。如果show.clusters = TRUE，实线绘制在聚类的边缘。


参数：...
additional arguments to the barplot plotting function
barplot绘图功能的附加参数


Details

详情----------Details----------

Each cluster (column of bootobj) is represented by a color. The proportion of bootstrap resampled data sets in which an element appeared in that cluster determines the proportion of the bar for that element which is the corresponding color. As a key, the clusters are labeled on the right margin in text of the same color.
每个聚类（列bootobj）是由一种颜色代表。引导重采样的数据集的元素在聚类出现的比例确定相应的颜色，这是该元素的条形的比例。作为一个关键，在相同颜色的文本右边缘簇被标记。


值----------Value----------

The function bootplot has no value. It does generate a plot.
功能bootplot有没有价值。它产生的图。


注意----------Note----------

Thank you to Sandrine Dudoit <sandrine@stat.berkeley.edu> for her input and to Jenny Bryan for the original clusplot code.
谢谢她的输入和为原clusplot代码珍妮布莱恩的桑德琳Dudoit <sandrine@stat.berkeley.edu>。


作者（S）----------Author(s)----------


Katherine S. Pollard &lt;kpollard@gladstone.ucsf.edu&gt;



参考文献----------References----------




参见----------See Also----------

hopach, boothopach, bootmedoids, barplot
hopach，boothopach，bootmedoids，barplot


举例----------Examples----------


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="euclid")

#hopach clustering[hopach聚类]
clustresult<-hopach(mydata,dmat=mydist)

#bootstrap[引导]
myobj<-boothopach(mydata,clustresult)

#plots[图]
bootplot(myobj,clustresult,showclusters=FALSE)
bootplot(myobj,clustresult,labels=paste("Sample",LETTERS[1:25],sep=" "))

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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