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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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More visualizations for gene expression data

This recipe will present some interesting and useful visualizations for expression data. The visualizations or plots explained in this recipe are heatmaps, Venn diagrams, and volcano plots.

Getting ready

For all the plots, we will either use datasets already used in the chapter or create artificial data while explaining the steps.

How to do it…

To generate the different types of plots, perform the following steps:

  1. Start with heatmaps. From the Clustering microarray data recipe, use the generated clusters, namely, c.array and c.gene.
  2. To do a heatmap, use the following clustering.plot function of the EMA library and pass the previously mentioned clusters as an argument:
    > library(EMA)
    > clustering.plot(tree=c.array, ...

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