heatmap.2 {gplots} R Documentation

Enhanced Heat Map

Description

A heat map is a false color image (basically image(t(x))) with a dendrogram added to the left side and/or 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.

This heatmap provides a number of extensions to the standard R heatmap function.

Usage

heatmap.2 (x,

           # dendrogram control
Rowv = TRUE,
Colv=if(symm)"Rowv" else TRUE,
distfun = dist,
hclustfun = hclust,
dendrogram = c("both","row","column","none"),
symm = FALSE, # data scaling
scale = c("none","row", "column"),
na.rm=TRUE, # image plot
revC = identical(Colv, "Rowv"),
add.expr, # mapping data to colors
breaks,
symbreaks=min(x < 0, na.rm=TRUE) || scale!="none", # colors
col="heat.colors", # block sepration
colsep,
rowsep,
sepcolor="white",
sepwidth=c(0.05,0.05), # cell labeling
cellnote,
notecex=1.0,
notecol="cyan",
na.color=par("bg"), # level trace
trace=c("column","row","both","none"),
tracecol="cyan",
hline=median(breaks),
vline=median(breaks),
linecol=tracecol, # Row/Column Labeling
margins = c(5, 5),
ColSideColors,
RowSideColors,
cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
srtRow = NULL,
srtCol = NULL,
adjRow = c(0,NA),
adjCol = c(NA,0),
offsetRow = 0.5,
offsetCol = 0.5, # color key + density info
key = TRUE,
keysize = 1.5,
density.info=c("histogram","density","none"),
denscol=tracecol,
symkey = min(x < 0, na.rm=TRUE) || symbreaks,
densadj = 0.25, # plot labels
main = NULL,
xlab = NULL,
ylab = NULL, # plot layout
lmat = NULL,
lhei = NULL,
lwid = NULL, # extras
...
)

Arguments

x

numeric matrix of the values to be plotted.

Rowv

determines if and how the row dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and no reordering is done. If a dendrogram, then it is used "as-is", ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector.

Colv

determines if and how the column dendrogram should be reordered. Has the 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.

distfun

function used to compute the distance (dissimilarity) between both rows and columns. Defaults to dist.

hclustfun

function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms. Defaults to hclust.

dendrogram

character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured.

symm

logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.

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.

na.rm

logical indicating whether NA's should be removed.

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.

add.expr

expression that will be evaluated after the call to image. Can be used to add components to the plot.

breaks

(optional) Either a numeric vector indicating the splitting points for binning x into colors, or a integer number of break points to be used, in which case the break points will be spaced equally between min(x) and max(x).

symbreaks

Boolean indicating whether breaks should be made symmetric about 0. Defaults to TRUE if the data includes negative values, and to FALSE otherwise.

col

colors used for the image. Defaults to heat colors (heat.colors).

colsep, rowsep, sepcolor

(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color sepcolor.

sepwidth

(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box drawn by colsep and rowsep as a function of the width (colsep) or height (rowsep) of a cell. Defaults to c(0.05, 0.05)

cellnote

(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols.

notecex

(optional) numeric scaling factor for cellnote items.

notecol

(optional) character string specifying the color for cellnote text. Defaults to "green".

na.color

Color to use for missing value (NA). Defaults to the plot background color.

trace

character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'.

tracecol

character string giving the color for "trace" line. Defaults to "cyan".

hline, vline, linecol

Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by linecol. Horizontal lines are only plotted if trace is 'row' or 'both'. Vertical lines are only drawn if trace 'column' or 'both'. hline and vline default to the median of the breaks, linecol defaults to the value of tracecol.

margins

numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.

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.

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.

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.

labRow, labCol

character vectors with row and column labels to use; these default to rownames(x) or colnames(x), respectively.

srtRow, srtCol

angle of row/column labels, in degrees from horizontal

adjRow, adjCol

2-element vector giving the (left-right, top-bottom) justification of row/column labels (relative to the text orientation).

offsetRow, offsetCol

Number of character-width spaces to place between row/column labels and the edge of the plotting region.

key

logical indicating whether a color-key should be shown.

keysize

numeric value indicating the size of the key

density.info

character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key.

denscol

character string giving the color for the density display specified by density.info, defaults to the same value as tracecol.

symkey

Boolean indicating whether the color key should be made symmetric about 0. Defaults to TRUE if the data includes negative values, and to FALSE otherwise.

densadj

Numeric scaling value for tuning the kernel width when a density plot is drawn on the color key. (See the adjust parameter for the density function for details.) Defaults to 0.25.

main, xlab, ylab

main, x- and y-axis titles; defaults to none.

lmat, lhei, lwid

visual layout: position matrix, column height, column width. See below for details

...

additional arguments passed on to image

Details

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).

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 NULL, no reordering will be done for
the corresponding side.

If 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.

The default colors range from red to white (heat.colors) and
are not pretty. Consider using enhancements such
as the RColorBrewer package,
http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer
to select better colors.

By default four components will be displayed in the plot. At the top
left is the color key, top right is the column dendogram, bottom left
is the row dendogram, bottom right is the image plot. When
RowSideColor or ColSideColor are provided, an additional row or column
is inserted in the appropriate location. This layout can be
overriden by specifiying appropriate values for lmat,
lwid, and lhei. lmat controls the relative
postition of each element, while lwid controls the column
width, and lhei controls the row height. See the help page for
layout for details on how to use these
arguments.

Value

Invisibly, a list with components

rowInd

row index permutation vector as returned by
order.dendrogram.

colInd

column index permutation vector.

call

the matched call

rowMeans, rowSDs

mean and standard deviation of each row: only
present if scale="row"

colMeans, colSDs

mean and standard deviation of each column: only
present if scale="column"

carpet

reordered and scaled 'x' values used generate the main
'carpet'

rowDendrogram

row dendrogram, if present

colDendrogram

column dendrogram, if present

breaks

values used for color break points

col

colors used

vline

center-line value used for column trace, present only if
trace="both" or trace="column"

hline

center-line value used for row trace, present only if
trace="both" or trace="row"

colorTable

A three-column data frame providing the lower and upper
bound and color for each bin

Note

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.

heatmap.2() 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.

Author(s)

Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
G. Warnes, revisions.

See Also

hclust

Examples

 library(gplots)
data(mtcars)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x), start=0, end=.3) ##
## demonstrate the effect of row and column dendogram options
##
heatmap.2(x) ## default - dendrogram plotted and reordering done.
heatmap.2(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
heatmap.2(x, dendrogram="col") ## col dendrogram plotted and col reordering done. heatmap.2(x, keysize=2) ## default - dendrogram plotted and reordering done. heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generate warning!
heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning! ## Show effect of row and column label rotation
heatmap.2(x, srtCol=NULL)
heatmap.2(x, srtCol=0, adjCol = c(0.5,1) )
heatmap.2(x, srtCol=45, adjCol = c(1,1) )
heatmap.2(x, srtCol=135, adjCol = c(1,0) )
heatmap.2(x, srtCol=180, adjCol = c(0.5,0) )
heatmap.2(x, srtCol=225, adjCol = c(0,0) ) ## not very useful
heatmap.2(x, srtCol=270, adjCol = c(0,0.5) )
heatmap.2(x, srtCol=315, adjCol = c(0,1) )
heatmap.2(x, srtCol=360, adjCol = c(0.5,1) ) heatmap.2(x, srtRow=45, adjRow=c(0, 1) )
heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) ) ## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is
## not also present)
heatmap.2(x, offsetRow=0, offsetCol=0)
heatmap.2(x, offsetRow=1, offsetCol=1)
heatmap.2(x, offsetRow=2, offsetCol=2)
heatmap.2(x, offsetRow=-1, offsetCol=-1) heatmap.2(x, srtRow=0, srtCol=90, offsetRow=0, offsetCol=0)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=1, offsetCol=1)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1) ##
## Show effect of z-score scaling within columns, blue-red color scale
##
hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030") ###
## Look at the return values
###
names(hv) ## Show the mapping of z-score values to color bins
hv$colorTable ## Extract the range associated with white
hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",] ## Determine the original data values that map to white
whiteBin <- unlist(hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",1:2])
rbind(whiteBin[1] * hv$colSDs + hv$colMeans,
whiteBin[2] * hv$colSDs + hv$colMeans )
##
## A more decorative heatmap, with z-score scaling along columns
##
hv <- heatmap.2(x, col=cm.colors(255), scale="column",
RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
xlab="specification variables", ylab= "Car Models",
main="heatmap(<Mtcars data>, ..., scale=\"column\")",
tracecol="green", density="density")
## Note that the breakpoints are now symmetric about 0 data(attitude)
round(Ca <- cor(attitude), 2)
symnum(Ca) # simple graphic # with reorder
heatmap.2(Ca, symm=TRUE, margin=c(6, 6), trace="none" ) # without reorder
heatmap.2(Ca, Rowv=FALSE, symm=TRUE, margin=c(6, 6), trace="none" ) ## Place the color key below the image plot
heatmap.2(x, lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(1.5, 4, 2 ) ) ## Place the color key to the top right of the image plot
heatmap.2(x, lmat=rbind( c(0, 3, 4), c(2,1,0 ) ), lwid=c(1.5, 4, 2 ) ) ## For variable clustering, rather use distance based on cor():
data(USJudgeRatings)
symnum( cU <- cor(USJudgeRatings) ) hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
distfun=function(c) as.dist(1 - c), trace="none") ## The Correlation matrix with same reordering:
hM <- format(round(cU, 2))
hM # now with the correlation matrix on the plot itself heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
distfun=function(c) as.dist(1 - c), trace="none",
cellnote=hM) ## genechip data examples
## Not run:
library(affy)
data(SpikeIn)
pms <- SpikeIn@pm # just the data, scaled across rows
heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
xlab="Relative Concentration", ylab="Probeset",
scale="row") # fold change vs "12.50" sample
data <- pms / pms[, "12.50"]
data <- ifelse(data>1, data, -1/data)
heatmap.2(data, breaks=16, col=redgreen, tracecol="blue",
main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
xlab="Relative Concentration", ylab="Probeset") ## End(Not run)

[Package gplots version 2.12.1 Index]
 
ref:
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/gplots/html/heatmap.2.html
 
http://bbsunchen.iteye.com/blog/1271580

heatmap.2的更多相关文章

  1. 基于HTML5实现3D热图Heatmap应用

    Heatmap热图通过众多数据点信息,汇聚成直观可视化颜色效果,热图已广泛被应用于气象预报.医疗成像.机房温度监控等行业,甚至应用于竞技体育领域的数据分析. http://www.hightopo.c ...

  2. 【JS】heatmap.js v1.0 到 v2.0,详细总结一下:)

    前段时间,项目要开发热力图插件,研究了heatmap.js,打算好好总结一下. 本文主要有以下几部分内容: 部分源码理解 如何迁移到v2.0 v2.0官方文档译文 关于heatmap.js介绍,请看这 ...

  3. funsioncharts的图表操作heatmap

    网址:http://www.fusioncharts.com/dev/chart-guide/heat-map-chart/introduction.html 以下只是假数据,目前还没有实现动态数据获 ...

  4. 用Excel制作热图(heatmap)的方法

    http://jingyan.baidu.com/article/64d05a0240ec75de55f73bd8.html 利用Excel 2010及以上版本的"条件格式"--& ...

  5. Heatmap.js v2.0 – 最强大的 Web 动态热图

    Heatmap 是用来呈现一定区域内的统计度量,最常见的网站访问热力图就是以特殊高亮的形式显示访客热衷的页面区域和访客所在的地理区域的图示.Heatmap.js 这个 JavaScript 库可以实现 ...

  6. R实战之热点图(HeatMap)

    快速实现是搜索帮助文档的首要目的,所以此处涉及实战的文章一概略去传统帮助文档的理论部分,直接上代码加注释! 本文将介绍R语言下利用ggplot2包制作heatmap的代码 -------------- ...

  7. 基于HTML5实现的Heatmap热图3D应用

    Heatmap热图通过众多数据点信息,汇聚成直观可视化颜色效果,热图已广泛被应用于气象预报.医疗成像.机房温度监控等行业,甚至应用于竞技体育领域的数据分析. 已有众多文章分享了生成Heatmap热图原 ...

  8. 网页热力图 heatmap js

    HBuilder +js 实现网页热力图 废话不多说,上代码 <!DOCTYPE html> <html> <head> <title>111</ ...

  9. Leaflet+heatmap实现离线地图加载和热力图应用

    本人博客主页:http://www.cnblogs.com/webbest/ 2017年春节已经过完,新一年的奋斗也刚刚开始.今年要经历的挑战也是大大的...不扯了. 年底前软件项目相对较多,恰巧在年 ...

随机推荐

  1. iOS多线程GCD 研究

    Grand Central Dispatch (GCD)是Apple开发的一个多核编程的解决方法. dispatch queue分成以下三种: 1)运行在主线程的Main queue,通过dispat ...

  2. CP="CAO PSA OUR" 用P3P header解决iframe跨域访问cookie

    1.IE浏览器iframe跨域丢失Session问题 在开发中,我们经常会遇到使用Frame来工作,而且有时是为了跟其他网站集成,应用到多域的情况下,而Iframe是不能保存Session的因此,网上 ...

  3. composer的安装

    HomeGetting StartedDownloadDocumentationBrowse Packages Dependency management Declaring dependencies ...

  4. ASP.NET Web – 输入的有效性验证

    下面这个示例显示了与文本框textFirstname相关的验证控件RequiredFieldValidator.所有的验证控件都有ErrorMessage和ControlToValidate属性.如果 ...

  5. 2815: [ZJOI2012]灾难 - BZOJ

    题目描述 Description 阿米巴是小强的好朋友.    阿米巴和小强在草原上捉蚂蚱.小强突然想,如果蚂蚱被他们捉灭绝了,那么吃蚂蚱的小鸟就会饿死,而捕食小鸟的猛禽也会跟着灭绝,从而引发一系列的 ...

  6. Nginx 301重定向域名

    为何要使用301重定向 在网站建设中需要网页重定向的情况很多:如网页目录结构变动,网页重命名.网页的扩展名改变.网站域名改变等.如果不做重定向,用户的收藏和搜索引擎数据库中的旧地址只能让访客得到一个4 ...

  7. Winform 窗体的操作

    原文:http://www.cnblogs.com/Billy-rao/archive/2012/05/16/2503437.html 怎样能使winform窗体的大小固定住,不能调整其大小 窗体Fo ...

  8. poj 2387 Til the Cows Come Home (最短路,dijkstra模版题)

    题目 #define _CRT_SECURE_NO_WARNINGS #include<string.h> #include<stdio.h> #include<math ...

  9. 转一篇:文档笔记之Django QuerySet

    这个放着,说不定以后作一些更深入的查询时,用得着的. http://www.rapospectre.com/blog/7/ 今天刚刚答完辩体完检就跑来更新博客了!!! 先补上第一篇: 一般情况下,我们 ...

  10. dynamic介绍

    Visual C# 2010 引入了一个新类型 dynamic. 该类型是一种静态类型,但类型为 dynamic 的对象会跳过静态类型检查. 大多数情况下,该对象就像具有类型 object 一样. 在 ...