heatmap(aCGH)
heatmap()所属R语言包：aCGH
Creates heatmap array CGH objects
创建热图阵列比较基因组杂交对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Clusters samples and produces heatmapp of the observed log2ratios.
聚类样品和产生观察log2ratios heatmapp。
用法----------Usage----------
heatmap(x, imp = TRUE, Rowv = NA, Colv = NULL, distfun = dist,
hclustfun = hclust, add.expr, symm = FALSE,
revC = identical(Colv, "Rowv"), scale = "none",
na.rm = TRUE, margins = c(5, 5), ColSideColors,
RowSideColors, cexRow = 0.2 + 1 / log10(nr),
cexCol = 0.2 + 1 / log10(nc), labRow = NULL,
labCol = NULL, main = NULL, xlab = NULL, ylab = NULL,
verbose = getOption("verbose"), methodR = "ward",
methodC = "ward", zlm = c(-0.5, 0.5), ...)
参数----------Arguments----------
参数：x
object of the aCGH object
对象aCGH对象的
参数：imp
logical variable indicating whether log2.ratios.imputed or log2.ratios slot of aCGH should be used. Defaults to imputed value (TRUE).
逻辑变量表示是否log2.ratios.imputed或log2.ratios插槽aCGH应使用。默认为估算值（TRUE）。
参数：Rowv
determines if and how the row dendrogram should be computed and reordered. Either a 'dendrogram' or a vector of values used to reorder the row dendrogram or 'NA' to suppress any row dendrogram (and reordering) or by default, 'NULL'
决定是否和如何计算和重新排列行聚类分析应。无论“树状图”或用来重新排列行树状或“不适用”压制任何行聚类分析和重新排序或默认值的向量，“空”
参数：Colv
determines if and how the column dendrogram should be reordered. Has the same options as the Rowv argument above and additionally when x is a square matrix, Colv = "Rowv" means that columns should be treated identically to the rows.
决定是否以及如何重新排序列树状应。 Rowv上述论点和另外有相同的选项时，x是一个方阵，Colv = "Rowv"意味着列应被视为相同的行。
参数：distfun
function used to compute the distance (dissimilarity) between both rows and columns. Defaults to 'dist'.
函数用于计算行和列之间的距离（相异）。默认为dist的。
参数：hclustfun
function used to compute the hierarchical clustering when 'Rowv' or 'Colv' are not dendrograms. Defaults to 'hclust'
函数用来计算“Rowv或Colv不聚类层次聚类。默认为“hclust
参数：add.expr
expression that will be evaluated after the call to 'image'. Can be used to add components to the plot.
表达，将评估后的“形象”的呼叫。可用于将组件添加到图。
参数：symm
logical indicating if 'x' should be treated *symm*etrically; can only be true when 'x' is a square matrix.
逻辑指示是否应被视为X* SYMM * etrically;只能是真正的X是一个方阵。
参数：revC
logical indicating if the column order should be 'rev'ersed for plotting, such that e.g., for the symmetric case, the symmetry axis is as usual.
逻辑表示如果列的顺序应绘图，reversed的，例如，为对称的情况下，对称轴是像往常一样。
参数：scale
character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is "row" if symm false, and "none" otherwise.
如果值应行的方向或列方向，或无为本，缩放字符显示。如果symm假的，和“无”，否则默认的是“行”。
参数：na.rm
logical indicating whether 'NA”s should be removed.
逻辑表示“不适用”是否应该被删除。
参数：margins
numeric vector of length 2 containing the margins (see 'par(mar= *)') for column and row names, respectively.
数字矢量长度为2包含的利润（见“看齐（MAR = *）），分别列名和列名。
参数：ColSideColors
(optional) character vector of length 'ncol(x)' containing the color names for a horizontal side bar that may be used to annotate the columns of 'x'.
（可选）特征向量长度（X）“NCOL水平的侧栏，可用于x的注释列包含的颜色名称。
参数：RowSideColors
(optional) character vector of length 'nrow(x)' containing the color names for a vertical side bar that may be used to annotate the rows of 'x'.
（可选）特征向量长度的NROW（X）“包含一个垂直的边栏，可以使用x的注释行的颜色名称。
参数：cexRow, cexCol
positive numbers, used as 'cex.axis' in for the row or column axis labeling. The defaults currently only use number of rows or columns, respectively.
正数，为“cex.axis行或列轴标签使用。目前默认只使用行或列数，分别。
参数：labRow, labCol
character vectors with row and column labels to use; these default to 'rownames(x)' or 'colnames(x)', respectively.
行和列标签使用这些默认到“rownames的特征向量（X）或colnames（X）”，分别。
参数：main, xlab, ylab
main, x- and y-axis titles;
主，X和Y轴标题;
参数：verbose
logical indicating if information should be printed.
逻辑说明是否应印信息。
参数：methodR
method to use for clustering rows. defaults to "ward"
聚类行的使用方法。默认为“病房”
参数：methodC
method to use for clustering columns. defaults to "ward"
聚类列使用方法。默认为“病房”
参数：zlm
all the values greater or equal than zlm are set to zlm - 0.01. a;; value less or equal to -zlm are set to -zlm + 0.01
所有值大于或等于比ZLM设置ZLM - 0.01。 ;;值小于或等于-ZLM设置到-ZLM + 0.01
参数：...
additional arguments passed on to 'image', e.g., 'col' specifying the colors.
额外的参数传递到“形象”，例如，col的指定颜色。
Details
详情----------Details----------
This function is almost identical to the heatmap in base R. The slight modifications are that (1) a user can specify clustering method for rows and columns; (2) all the values outside specified limits are floored to be 0.01 less than a limit; (3) default values are different. Note that using default option of imp (TRUE) produces nicer looking plots as all missing values are removed.
此功能几乎是相同的heatmap在碱基R.稍作修改：（1）用户可以指定行和列的聚类方法;（2）以外的所有指定的限制值是地板少0.01超过限额;（3）默认值是不同的。注意imp（TRUE），使用默认选项更好看的图产生的所有缺失值被删除。
值----------Value----------
Invisibly, a list with components
无形之中，一个组件的列表
参数：crowInd
row index permutation vector as returned by order.dendrogram
行指数排列向量order.dendrogram返回
参数：colInd
row index permutation vector as returned by order.dendrogram
行指数排列向量order.dendrogram返回
参考文献----------References----------
<h3>See Also</h3> <code>aCGH</code> <code>clusterGenome</code>
举例----------Examples----------
#default plotting method for the aCGH object[aCGH对象的默认绘制方法]
data(colorectal)
plot(colorectal)
#to produce smoother looking heatmap, use imp = T: this will use imputed[生产顺畅寻找热图，使用imp = T：这将使用归咎于]
#slot of aCGH object[插槽aCGH对象]
plot(colorectal, imp = TRUE)
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 10:59:59
