本篇文章介绍R语言默认热图函数heatmap
### 准备工作
rm(list = ls())
getwd()
setwd("/Users/xuefei/Documents/Heatmap1/")
dir()
# 测试数据
a=c(12,14,17,11,16)
b=c(4,20,15,11,9)
c=c(5,7,19,8,18)
d=c(15,13,11,17,16)
e=c(12,19,16,7,9)
A=cbind(a,b,c,d,e)
B=rbind(a,b,c,d,e)
首先我们阅读了说明书（文章最后）
#代码1
require(graphics); require(grDevices)
x <- as.matrix(A)
rc <- rainbow(nrow(x), start = 0, end = .3)
cc <- rainbow(ncol(x), start = 0, end = .3)
hv <- heatmap(x, col = cm.colors(256), scale = "column",
RowSideColors = rc, ColSideColors = cc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<BIOTREE>, ..., scale = \"column\")")
utils::str(hv)
代码1
#代码2
## no column dendrogram (nor reordering) at all:
## 完全没有列树图(或重新排序)：
heatmap(A, Colv = NA, col = cm.colors(256), scale = "column",
RowSideColors = rc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
代码2
#代码3
## "no nothing"
heatmap(A, Rowv = NA, Colv = NA, scale = "column",
main = "heatmap(*, NA, NA) ~= image(t(x))")
round(Ca <- cor(attitude), 2)
symnum(Ca) # simple graphic
heatmap(Ca, symm = TRUE, margins = c(6,6)) # with reorder()
heatmap(Ca, Rowv = FALSE, symm = TRUE, margins = c(6,6)) # _NO_ reorder()
代码3
#代码4
## slightly artificial with color bar, without and with ordering:
## 略人工加色条，无且有顺序:
cc <- rainbow(nrow(Ca))
heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, ColSideColors = cc,
margins = c(6,6))
heatmap(Ca, symm = TRUE, RowSideColors = cc, ColSideColors = cc,
margins = c(6,6))
代码4
——————** heatmap说明书**—————
Draw a Heat Map
Description #介绍
A heat map is a false color image (basically image(t(x))) with a dendrogram added to the left side and to the top. Typically, reordering of the rows and columns according to some set of values (row or column means) within the restrictions imposed by the dendrogram is carried out.
热图是一种假彩色图像(基本上是图像(t(x))，在左侧和顶部添加树状图。通常，在树状图所施加的限制内，根据某些值(行或列表示)重新排序行和列。
Usage #使用
heatmap(x, Rowv = NULL, Colv = if(symm)"Rowv" else NULL,
distfun = dist, hclustfun = hclust,
reorderfun = function(d, w) reorder(d, w),
add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
scale = c("row", "column", "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,
keep.dendro = FALSE, verbose = getOption("verbose"), ...)
Arguments #参数
x
numeric matrix of the values to be plotted.
# 要绘制的值的数值矩阵
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, see ‘Details’ below.
# 确定是否以及如何计算行树图并重新排序。一个树状图或一个值向量，用于重新排序行树状图或NA，以抑制任何行树状图(和重新排序)，或默认为空，请参见下面的“详细信息”。
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 (and so if there is to be no row dendrogram there will not be a column one either).
# 确定是否以及如何重新排序列树状图。与上面的Rowv参数有相同的选项，另外，当x是一个方阵时，Colv = "Rowv"意味着列应该与行同等对待(因此，如果没有行树图，也不会有列1)。
distfun
# 用于计算行和列之间的距离(不同)的函数。默认为dist。
hclustfun
function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms. Defaults to hclust. Should take as argument a result of distfun and return an object to which as.dendrogram can be applied.
# 当Rowv或Colv不是树状图时，用于计算层次聚类的函数。默认为hclust。应该将distfun的结果作为参数，并返回一个可以应用as.dendrogram的对象。
reorderfun
function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses reorder.dendrogram.
# 树状图的函数(d, w)和重排序行和列树状图的权值。默认使用reorder.dendrogram。
add.expr
expression that will be evaluated after the call to image. Can be used to add components to the plot.
# 在调用image之后将计算的表达式。可用于向绘图添加组件。
symm
logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.
# 逻辑指示是否对x进行对称处理;只有当x是方阵时才成立
revC
logical indicating if the column order should be reversed for plotting, such that e.g., for the symmetric case, the symmetry axis is as usual.
# 用于绘图的列顺序是否应该反转的逻辑指示，例如，对于对称情况，对称轴与往常一样。
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.
# 字符，指示值是否应该在行方向或列方向中居中和缩放，或不缩放。如果symm为false，默认为“row”，否则为“none”。
na.rm
logical indicating whether NA's should be removed.
# 逻辑指示是否应该删除NA。
margins
numeric vector of length 2 containing the margins (see par(mar = *)) for column and row names, respectively.
# 长度为2的数字向量，分别包含列名和行名的边距(参见par(mar = *))。
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)长度ncol(x)的字符向量，包含可用于注释x列的水平边栏的颜色名称。
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)长度为nrow(x)的字符向量，包含用于注释x行的垂直边栏的颜色名称。
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，用作cex。轴在为行或列轴标记。当前的默认值分别只使用行或列的数量。
labRow, labCol
character vectors with row and column labels to use; these default to rownames(x) or colnames(x), respectively.
# 使用行和列标签的字符向量;这些默认为rownames(x)或colnames(x)。
main, xlab, ylab
main, x- and y-axis titles; defaults to none.
# 主标题、x轴标题和y轴标题;默认为没有。
keep.dendro
logical indicating if the dendrogram(s) should be kept as part of the result (when Rowv and/or Colv are not NA).
# 逻辑指示树图是否应该作为结果的一部分保留(当Rowv和/或Colv不是NA时)。
verbose
logical indicating if information should be printed.
# 逻辑指示是否打印信息。
...
additional arguments passed on to image, e.g., col specifying the colors.
# 其他参数传递给图像，例如，col指定颜色。
Details #详细说明
If either Rowv or Colv are dendrograms they are honored (and not reordered). Otherwise, dendrograms are computed as dd <- as.dendrogram(hclustfun(distfun(X))) where X is either x or t(x).
# 如果Rowv或Colv都是树状图，它们将得到尊重(而不是重新排序)。否则，树状图被计算为dd <- as.树状图(hclustfun(distfun(X)))，其中X为X或t(X)
If either is a vector (of ‘weights’) then the appropriate dendrogram is reordered according to the supplied values subject to the constraints imposed by the dendrogram, by reorder(dd, Rowv), in the row case. If either is missing, as by default, then the ordering of the corresponding dendrogram is by the mean value of the rows/columns, i.e., in the case of rows, Rowv <- rowMeans(x, na.rm = na.rm). If either is NA, no reordering will be done for the corresponding side.
#如果其中一个向量(“权值”)，那么适当的树状图将根据树状图施加的约束(dd, Rowv)，在行情况下根据树状图提供的值重新排序。如果其中任何一个缺失(默认情况下)，那么相应树状图的顺序就是行/列的平均值，即，对于行，Rowv <- rowMeans(x, na)。rm = na.rm)。如果其中任何一个是NA，则不需要对对应的一侧进行重新排序。
By default (scale = "row") the rows are scaled to have mean zero and standard deviation one. There is some empirical evidence from genomic plotting that this is useful.
# 默认情况下(scale = "row")，这些行被缩放到均值为零，标准差为1。有一些来自基因组绘图的经验证据表明这是有用的。
The default colors are not pretty. Consider using enhancements such as the RColorBrewer package.
# 默认的颜色并不漂亮。考虑使用增强功能，例如RColorBrewer package。
Value
Invisibly, a list with components
# 不可见的，包含组件的列表
rowInd
row index permutation vector as returned by order.dendrogram.
# 由order.dendrogram返回的行索引排列向量。
colInd
column index permutation vector.
# 列索引排列向量。
Rowv
the row dendrogram; only if input Rowv was not NA and keep.dendro is true.
# 行系统树图;只有输入Rowv不是NA和keep。dendro是真的。
Cold
the column dendrogram; only if input Colv was not NA and keep.dendro is true.
列系统树图;只有当输入Colv不是NA和keep时，dendro才是正确的。
Note
Unless Rowv = NA (or Colw = NA), the original rows and columns are reordered in any case to match the dendrogram, e.g., the rows by order.dendrogram(Rowv) where Rowv is the (possibly reorder()ed) row dendrogram.
# 除非Rowv = NA(或Colw = NA)，否则原始的行和列在任何情况下都会被重新排序以匹配树状图，例如，按顺序排列的行。
heatmap() uses layout and draws the image in the lower right corner of a 2x2 layout. Consequentially, it can not be used in a multi column/row layout, i.e., when par(mfrow = *) or (mfcol = *) has been called.
# heatmap()使用布局并在一个2x2布局的右下角绘制图像。因此，它不能用于多列/行布局，即，当par(mfrow = *)或(mfcol = *)被调用时。
Author(s)
Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber, revisions.
# 安迪•Liaw原始;先生，M. Maechler, W. Huber，修订。
See Also #另请参阅
image, hclust
Examples ## 示例，非常重要
require(graphics); require(grDevices)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start = 0, end = .3)
cc <- rainbow(ncol(x), start = 0, end = .3)
hv <- heatmap(x, col = cm.colors(256), scale = "column",
RowSideColors = rc, ColSideColors = cc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
utils::str(hv) # the two re-ordering index vectors
image.png
## no column dendrogram (nor reordering) at all:
## 完全没有列树图(或重新排序)：
heatmap(x, Colv = NA, col = cm.colors(256), scale = "column",
RowSideColors = rc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
## "no nothing"
heatmap(x, Rowv = NA, Colv = NA, scale = "column",
main = "heatmap(*, NA, NA) ~= image(t(x))")
round(Ca <- cor(attitude), 2)
symnum(Ca) # simple graphic
heatmap(Ca, symm = TRUE, margins = c(6,6)) # with reorder()
heatmap(Ca, Rowv = FALSE, symm = TRUE, margins = c(6,6)) # _NO_ reorder()
## slightly artificial with color bar, without and with ordering:
## 略人工加色条，无且有顺序:
cc <- rainbow(nrow(Ca))
heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, ColSideColors = cc,
margins = c(6,6))
heatmap(Ca, symm = TRUE, RowSideColors = cc, ColSideColors = cc,
margins = c(6,6))
## 对于变量聚类，使用基于cor()的距离:
symnum( cU <- cor(USJudgeRatings) )
hU <- heatmap(cU, Rowv = FALSE, symm = TRUE, col = topo.colors(16),
distfun = function(c) as.dist(1 - c), keep.dendro = TRUE)
## The Correlation matrix with same reordering:
## 相同重排序的相关矩阵:
round(100 * cU[hU[[1]], hU[[2]]])
## The column dendrogram:
## 列树图:
utils::str(hU$Colv)
