Making Heatmaps

Load the data

The data can be prepared in csv or text file to load the data in to R. For example, to load list.csv:

data <- read.csv (“list.csv”)

Name the rows

You can then name the rows of the heatmap like so:

Row.names(data) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

Type:Data <- data [,2: n]

In the above command, n is the number of columns to be included in the heat map.

Build a data matrix

Use the following command to build a data matrix for making the heat map:

Data_matrix <- data.matrix (data)

Plot the heat map

Note: Gnuplot package must be installed in R before heat maps may be displayed! Run the following command to load in the gplots library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (Data_matrix, dendrogram="row", col= redgreen (75), scale="none", key = TRUE, keysize = 1.0, margins = c(4,30),  density.info="none", trace="none")