Heatmap Gene Expression Visualization

Heatmap and Dendrogram visualization of the normalized gene expression using hierarchical clustering

<Heatmap>
The gene expression data is displayed by colored squares in the heatmap.
Green : Up-regulation
Black : UNchanged expression
Red : Down-regulation

<Dendrogram>
The dendrogram visualizes hierarchical clusting result which build a hierarchy of clusters.

Screenshot

Parameter : Data - Spellman (30), Cluster Parameter - single, Axis - Both, Color - RGB

Parameter : Data - Spellman (30), Cluster Parameter - complete, Axis - Both, Color - ROY

Parameter : Data - Spellman (30), Cluster Parameter - median, Axis - Both, Color - RWB

Setup

Prerequisites

• Python 3.5+
• scipy 0.18.1
• pandas 0.18.1
• numpy 1.12.1

Reference

• Hierarchical Clustering and Heatmap : http://blog.nextgenetics.net/?e=44
• Dendrogram : http://bl.ocks.org/mbostock/4063570
• Data : http://www.exploredata.net/Downloads/Gene-Expression-Data-Set