Overview

The heatmap tool creates a heatmap of the gene list and sample selection.

Basic Usage

On page load, a heatmap is created with default settings. There are options to change the distance measure and clustering methods, turn dendrogram/clustering on and off for samples and genes (by default, only genes are clustered).

Example work flow:

1. Add genes to the genelist.
2. Go to exHeatmap to create a heatmap.
3. Select which dimensions to cluster and display dendrogram for:  samples (x-axis) and/or genes (y-axis).
4. Select cluster function and distance methods.

Data

There are currently two expression tables in our database for PopGenIE (All affymetrix or Asp201 Expression Atlas) and one each for ATGenIE and ConGenIE.

Implementation

The heatmap tool is implemented in python with the rpy package. The heatmap is created with the R gplots.heatmap2. The website is coded with HTML, PHP and JavaScript.

Standard Score 

You can read more about the standard score here.