Making Heatmaps: Difference between revisions

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


  Row.names(data) <- data$Name
  row.names(data) <- data$Name


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


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


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

Revision as of 03:49, 17 August 2012

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:

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")