## Visualisation / Annotated heatmap

### Description

Visualizes the grouping of samples or genes as a static heatmap image. If you would like to have an interactive heatmap which scales well and allows to select genes, please run the tool "Clustering / Hierachical" and double-click on the result file hc.tre.

### Parameters

- Annotation column from the phenodata matrix [EMPTY]
- Number of groups to color to the tree [2]
- Coloring scheme (Red-Green, Red-Black-Green, Red-White-Blue, Black-White) [Green-Red]
- Cluster samples only [no]
- Scale data [row]
- Distance [pearson]
- Agglomeration method to be used in clustering [average]
- Image width (200-3200) [600]
- Image height (200-3200) [600]

### Details

First both chips and genes are clustered using the chosen distance metric and agglomeration method. These clusterings are then visualized as a heatmap, where every gene on every chip is colored according to its expression level in the data. Please note that while this tool can be applied to a dataset containing up 20 000 genes/samples, the text doesn't scale accordingly. For large data sets it is recommended to use the "Clustering / Hierachical " tool instead.

Sample annotation information can be added by setting the annotation column to something else than EMPTY. Currently, sample information such as annotation or experimental group and mean values can be added to plot.

The tool also automatically splits the tree into a specified number of groups, and visualizes the dendrogram leading to these groups with different colors, if number of groups to color to the tree is set to something higher than 0.

### Output

A color PNG image containing the heatmap: