heatmap_plus(Heatplus)
heatmap_plus()所属R语言包：Heatplus
Display an Annotated Heatmap
显示注释的热图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function displays an expression data matrix as a heatmap with a column dendrogram. A given clustering will be shown in color. Additionally, a number of binary and interval scaled covariates can be added to characterize these clusters.
此功能显示，与一列树状热图表达数据矩阵。颜色将显示在一个给定的聚类。此外，一些二进制和间隔规模变项可以被添加到这些聚类的特点。
This function is just about to be deprecated. Please use functions annHeatmap or annHeatmap2 for new projects.
此功能只是被废弃。请使用功能annHeatmap或annHeatmap2新项目。
用法----------Usage----------
heatmap_plus(x, addvar, covariate = NULL, picket.control = list(), h, clus,
cluscol, cluslabel = NULL, Rowv, Colv, reorder = c(TRUE, TRUE),
distfun = dist, hclustfun = hclust, scale = c("row", "column",
"none"), na.rm = TRUE, do.dendro = TRUE, col = heat.colors(12),
trim, equalize = FALSE, ...)
参数----------Arguments----------
参数：x
the numerical data matrix to be displayed.
要显示的数值数据矩阵。
参数：addvar
data frame with (mostly binary) covariates.
（主要是二进制）协变量的数据框。
参数：covariate
integer indicating the one column in addvar that is interval scaled.
addvar，一列整数，指示间隔缩放。
参数：picket.control
list of option for drawing the covariates, passed to oldPicketplot.
绘制协变量的选项列表，通过oldPicketplot。
参数：h
height at which to cut the dendrogram, as in oldCutree; overrides clus.
高度降低了聚类分析，如oldCutree;覆盖clus。
参数：clus
an explicit vector of cluster memberships for the columns of x, if no dendrogram is used; ignored if do.dendro=TRUE and h is specified.
x，如果没有使用树状列，忽略do.dendro=TRUE和h指定聚类成员的明确向量。
参数：cluscol
a vector of colors used to indicate clusters.
用来指示聚类的颜色向量。
参数：cluslabel
labels to designate cluster names.
指定聚类名称的标签。
参数：Rowv
either a dendrogram or a vector of reordering indexes for the rows.
无论是树状图或行的重新排序指标的向量。
参数：Colv
either a dendrogram or a vector of reordering indexes for the columns.
无论是树状图或重新排序索引的列向量。
参数：reorder
logical vector of length two, indicating whether the rows and columns (in this order) should be reordered using order.dendrogram.
逻辑向量的长度为二，说明是否应重新安排使用order.dendrogram行和列（以这个顺序）。
参数：distfun
function to compute the distances between rows and columns. Defaults to dist.
函数来计算行和列之间的距离。 dist默认。
参数：hclustfun
function used to cluster rows and columns. Defaults to hclust.
用于聚类的行和列的功能。 hclust默认。
参数：scale
indicates whether values should be scaled by either by row, column, or not at all. Defaults to row.
指示值是否应要么缩减，由行，列，或根本没有。 row默认。
参数：na.rm
logical indicating whther to remove NAs.
逻辑表示whther删除NAS。
参数：do.dendro
logical indicating whether to draw the column dendrogram.
逻辑表明是否提请列树状。
参数：col
the color scheme for image. The default sucks.
为image颜色方案。默认的吮吸。
参数：trim
Percentage of values to be trimmed. This helps to keep an informative color scale, see Details.
值的百分比来进行修整。这有助于保持一个内容丰富的色阶，看到详细信息。
参数：equalize
logical indicating whther to use the ranks of the data for setting the color scheme; alternative to trim, see Details.
逻辑的指示whther设置配色方案中使用的数据的行列;替代trim，详细。
参数：...
extra arguments to image.
image额外的参数。
Details
详情----------Details----------
This is a heavily modified version of heatmap_2, which is a heavily modfied version of an old version of heatmap in package stats, so some of the arguments are described in more detail there. The main distinguishing feature of this routine is the possibility to color a cluster solution, and to add a covariate display.
这是一个严重的heatmap_2，这是一个旧版本的重modfied版本修改后的版本heatmap包stats，所以一些参数中有更详细的描述。这个程序的主要特点是颜色的聚类解决方案的可能性，并添加一个协显示器。
Covariates are assumed to be binary, coded as 0 and 1 (or FALSE and TRUE respectively). One of the covariates can be interval scaled, the column index of this variable is supplied via argument covariate. The details of the added display are handled by the function picketplot.
协变量被假设为二进制编码为0和1（或FALSE和TRUE）。的协变量可以是一个区间规模，这个变量的列索引提供通过参数covariate。增加显示器的细节处理功能picketplot。
Setting trim to a number between 0 and 1 uses equidistant classes between the (trim)- and (1-trim)-quantile, and lumps the values below and above this range into separate open-ended classes. If the data comes from a heavy-tailed distribution, this can save the display from putting too many values into to few classes. Alternatively, you can set equal=TRUE, which uses an equidistant color scheme for the ranks of the values.
设置trim0和1之间的数字之间使用等距离类（trim） - （1 - trim）位数，肿块低于和高于这个范围的值将单独开放式课程。如果数据从一个重尾分布，这样可以节省显示，从投入到少数几类值太多。另外，你可以设置的equal=TRUE，它使用的值的行列等距离的配色方案。
值----------Value----------
A list with components
与组件列表
参数：rowInd
indices of the rows of the display in terms of the rows of x.
x行指数显示行。
参数：colInd
ditto for the columns of the display.
同上，用于显示列。
参数：clus
the cluster indices of the columns of the display.
聚类指数显示列。
作者（S）----------Author(s)----------
Original by Andy Liaw, with revisions by Robert Gentleman and Martin Maechler.
Alexander Ploner for the modifications documented here.
参见----------See Also----------
heatmap_2, heatmap, oldPicketplot, oldCutplot.dendrogram,
heatmap_2，heatmap，oldPicketplot，oldCutplot.dendrogram
举例----------Examples----------
# create data[创建数据]
mm = matrix(rnorm(1000, m=1), 100,10)
mm = cbind(mm, matrix(rnorm(2000), 100, 20))
mm = cbind(mm, matrix(rnorm(1500, m=-1), 100, 15))
mm2 = matrix(rnorm(450), 30, 15)
mm2 = cbind(mm2, matrix(rnorm(900,m=1.5), 30,30))
mm=rbind(mm, mm2)
colnames(mm) = paste("Sample", 1:45)
rownames(mm) = paste("Gene", 1:130)
addvar = data.frame(Var1=rep(c(0,1,0),c(10,20,15)),
Var2=rep(c(1,0,0),c(10,20,15)),
Var3=rep(c(1,0), c(15,30)),
Var4=rep(seq(0,1,length=4), c(10,5,15,15))+rnorm(45, sd=0.5))
addvar[3,3] = addvar[17,2] = addvar[34,1] =NA
colnames(addvar) = c("Variable X","Variable Y", "ZZ","Interval")
# the lame default, without clustering[跛脚默认情况下，没有聚类]
# Labels do not look too hot that way[标签不看太热，方式]
heatmap_plus(mm)
# without labels, but with cluster[无标签，但与聚类]
dimnames(mm)=NULL
heatmap_plus(mm, h=40)
# add some covariates, with nice names[添加一些协变量，好听的名字]
heatmap_plus(mm, addvar=addvar, cov=4)
# covariates and clustering[协变量和聚类]
heatmap_plus(mm, addvar=addvar, cov=4, h=20, col=RGBColVec(64), equal=TRUE)
# Clustering without the dendrogram[没有的树状聚类]
cc = cutree(hclust(dist(t(mm))), k=5)
heatmap_plus(mm, addvar=addvar, cov=4, clus=cc, do.dendro=FALSE)
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 21:31:53
