How to draw heat map

Start "R", and change directory.

To change directory, you can choose the menu "change directory" on "R".

Please set your directory in the folder including your data-text file.

I attached the demo file below.

This file should be used as a tab-text format.

FYI, this demo file includes a series of circadian expressions of plant clock genes, CCA1, LHY, TOC1/PRR1, PRR3, PRR5, PRR7 and PRR9 (data from Edwards KD et al., 2006). You can also see it in our publication (Hanano S and Davis SJ, 2007).

# Open "genefilter" and "gplots" packages. * you need install these packages before you draw the heat-map.

> library(genefilter)

> library(gplots)

# Read data

> data <- read.delim("clockdemo.txt", header=TRUE, row.names=1)

# Draw heatmap with raw data

> heatmap(as.matrix(data), margin=c(4,8), main="Heat Map 1 (Raw Data)")

# Z Score

> data.z <- genescale(data, axis=1, method="Z")

# Heatmap from Z scored data

> heatmap(as.matrix(data.z), margin=c(4,8), main="Heat Map 2 (Z score Data)")

# Heatmap from Z scored data, with red-green color, and without column change.

> heatmap.2(as.matrix(data.z), col=greenred(75), scale="none", key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=1, margin=c(4,8), main="Heat Map 2 (Z score Data)", Colv=NA)

# Please ignore the "warning".

Warning message:

In heatmap.2(as.matrix(data.z), col = greenred(75), scale = "none", :

Discrepancy: Colv is FALSE, while dendrogram is `row'. Omitting column dendogram.

#

I referred to the following site.

だれでもできるマイクロアレイ解析

http://blogs.yahoo.co.jp/doshiroutomicroarray

P.S.

If you use 'col = cm.colors(100)' instead of col = greenred(75), you can use CM colors.

> heatmap.2(as.matrix(data.z), col = cm.colors(100), scale="none", key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=1, margin=c(4,8), main="Heat Map 2 (Z score Data)", Colv=NA)