annHeatmap2(Heatplus)
annHeatmap2()所属R语言包：Heatplus
Annotated heatmaps
注解热图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function plots a data matrix as intensity heatmap, with optional dendrograms, annotation panels and clustering for both rows and columns. This is the actual working function called by numerous wrappers.
此功能图强度热图作为数据矩阵，可选的聚类，注释行和列的面板和聚类。这是由众多的包装称为实际工作功能。
用法----------Usage----------
annHeatmap2(x, dendrogram, annotation, cluster, labels,
scale = c("row", "col", "none"), breaks=256, col = g2r.colors,
legend = FALSE)
参数----------Arguments----------
参数：x
the numerical matrix to be shown as heatmap
热图显示的数值矩阵
参数：dendrogram
a list that controls how row- and column diagrams are determined and displayed
行和列图是如何确定和显示控制列表
参数：annotation
a list that controls the data and the way it is shown in row- and column annotation panels
列表控制的数据行和列注释面板中的显示方式
参数：cluster
a list that controls how many clusters are chosen, and how these clusters are labelled and colored
控制多少聚类的选择，以及如何标记和颜色这些聚类列表
参数：labels
a list that controls the row- and column labels, as well as their size and placement
控制的行和列的标签，以及他们的大小和位置列表
参数：scale
a character string indicating how the matrix x is standardized (by row, by column or not at all). This affects only display, not dendrograms or clustering
一个字符串，指示如何矩阵x是标准化（按行，列或根本不）。这会影响只显示，树状图或聚类
参数：breaks
specifies the interval breaks for displaying the data in x; either a vector of explicit interval breaks, or just the desired number of intervals. See niceBreaks for details.
数据显示指定的时间间隔截断x无论是明确的间隔时间，或只是所需的时间间隔数向量。看到niceBreaks详情。
参数：col
specifies a palette of colors for the heatmap intensities; either a vector of explicit color definitions (one less than breaks) or a palette function. See breakColors.
指定一个热图强度的颜色调色板，无论是明确的颜色定义矢量（比截断少）或调色板功能。看到breakColors。
参数：legend
whether and where to draw a legend for the colors/intervals in the heatmap. If TRUE, a legend is placed in a position determined by the function to be suitable; alternatively, integer values 1-4 indicate the side where the legend is to be drawn; and FALSE indicates that no legend should be drawn.
是否以及在何处的颜色/间隔在热图绘制一个传奇。如果TRUE，传说被放置在由功能决定的，是合适的位置，或者，“1-4的整数值表示边，传说是要绘制;FALSE表示，没有传说应当制定。
Details
详情----------Details----------
Arguments scale, breaks, col and legend control different aspects of the whole plot directly as described. Arguments dendrogram, annotation, cluster and labels control aspects that may differ for the rows and columns of the central heatmap and have a special structure: each is a named list with different entries controling e.g. the look of a dendrogram, the data for annotation etc. Additionally, they can contain two extra entries called simply Row and Col; these are again named lists that can contain all the same entries as the parent list. Entries specified directly in the list apply to both rows and columns; entries specified as part of Row or Col override these defaults for the rows or columns only.
参数scale，breaks，col和legend控制整个图的不同方面直接描述。参数dendrogram，annotation，cluster和labels控制方面，可能会有所不同，中央热图的行和列，并有特殊的结构：每一个命名名单不同的条目温控如注释等数据聚类的外观，此外，他们可以包含两个额外的条目，只需Row和Col;再次命名列表，可以包含所有相同的父列表条目。直接在列表中指定的条目适用于行和列;作为Row或Col覆盖这些默认的行或列的一部分指定的条目。
Recognized parameters for argument dendrogram:
确认参数参数dendrogram：
clustfun the clustering function for generating the dendrogram; defaults to hclust for rows and columns
clustfun生成树状图的聚类功能，行和列默认为hclust
distfun a function that returns the pairwise distances between samples/features as an object of class dist; defaults to dist for rows and columns
distfun一个函数返回一个对象类的dist成对样本/功能之间的距离;默认的行和列dist
status a string that controls the display of the dendrogram: yes means use the dendrogram to re-order the rows/columns and display the dendrogram; hidden means re-rorder, but do not display; no means do not use the dendrogram at all.
状态控制的聚类分析显示：yes意味着使用重新排序的行/列的树状显示树状图;hidden意味着重新rorder的，但不显示;<字符串x>手段不使用树状。
dendro an override argument that allows to pass in a dendrogram directly, bypassing the clustfun and distfun mechanism; defaults to NULL (i.e. is not used)
dendro重写参数，可以通过直接在树状图，绕过clustfun和distfun机制;默认NULL（即不使用）
Recognized entries for argument annotation:
确认参数项annotation：
data a data frame containing the annotation data; defaults to NULL, i.e. no annotation is displayed
数据一个数据框包含注释的数据;默认NULL，即没有标注显示
control a list of fine-tuning parameters that is passed directly to picketPlot; defaults to an empty list, i.e. the default settings in picketPlot
微调参数控制列表被直接传递到picketPlot;默认为一个空列表，即picketPlot默认设置
asIs logical value indicating whether the annotation data needs to be pre-processed via convAnnData or not; defaults to TRUE
ASIS逻辑值，指明是否注释data需要通过convAnnData或不预先处理;默认TRUE
inclRef logical value indicating whether to include all levels of factor variables in data, or whether to drop the reference level (i.e. the first level). Defaults to TRUE
inclRef逻辑值，指明是否包括在data，还是下降的参考电平（即第一级）各级因子变量。 TRUE默认
Recognized entries for argument cluster:
确认参数项cluster：
cuth the height at which to cut through the dendrogram to define groups of similar features/samples; defaults to NULL, i.e. no cutting
cuth的高度时，通过聚类削减定义类似的功能/样品组默认NULL，即无切削
label labels for the clusters; defaults to NULL, i.e. no labels
标签标签聚类; NULL默认，即无标签
col colors for the different clusters; the colors are used for coloring both the sub-trees of the dendrogram and the corresponding area in the annotation plot (if there is one). This is either a vector of colors, or a palette function that takes a number and returns a vector of colors of the specified length; defaults to RainbowPastel
的山坳颜色不同的聚类;颜色着色的聚类分析和注释图相应区域的子树（如果有）。这是一个向量，颜色或调色板功能，需要一个数字，并返回一个指定长度的颜色向量;默认为RainbowPastel
grp an override argument that directly specifies group memberships for the features/samples, completely bypassing the whole dendrogram and cuth mechanism. This probably only works for dendrogram$status="no".
GRP重写参数直接指定的功能/样本组成员，完全绕过整个dendrogram和cuth机制。 dendrogram$status="no"这大概只有作品。
Recognized entries for argument labels:
确认参数项labels：
cex size of the text for the labels; defaults to NULL, i.e. use a hard-coded default guess
CEX为标签的文字大小，默认为NULL，即使用一个硬编码的默认猜测
nrow amount of space available for the labels between the central heatmap and the dendrogram, expressed as lines of text; defaults to 3.
的NROW之间的中央热图和树状标签的可用空间量，表现为文本行;默认为3。
side side at which to draw the labels, coded as integer between 1 and 4 in the usual way (1 = below the plot, continuing clockwise). A common default for rows and columns does not make sense: rows only work with 2 and 4, columns only with 1 and 3. Defaults try to make use of empty space, depending on the presence of a dendrogram.
并排在绘制标签，编码为1和4之间的整数，通常的方法（1 =下面的图，持续顺时针方向）。一个共同默认的行和列没有道理：行只有2和4，列只有1和3。默认尝试使用空的空间，根据存在树状。
labels labels for rows and columns; defaults to NULL, i.e. using the row- and column names of x.
标签，标签的行和列;默认NULL，即使用x行和列名。
值----------Value----------
An object of class annHeatmap. Use plot to display it graphically.
对象类annHeatmap。使用plot图形显示。
参见----------See Also----------
heatmapLayout, niceBreaks, breakColors, g2r.colors
heatmapLayout，niceBreaks，breakColors，g2r.colors
举例----------Examples----------
require(Biobase)
data(sample.ExpressionSet)
ex1 = sample.ExpressionSet[51:85,]
map1 = annHeatmap2(exprs(ex1), ann=list(Col=list(data=pData(ex1))),
cluster=list(Col=list(cuth=3000)))
plot(map1)
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 21:30:30
