The core interface in Morpheus is a heat map, in which a matrix of values is mapped to a matrix of colors. Heat maps are one of the most widely used visualizations in the sciences because they allow you to find patterns in your data, compact a large amount of information into a small space, and are a natural representation of a matrix.

Import Data

Select File > Open to import data.


Matrices can be imported from GCT 1.3, GCT 1.2, MAF, GMT, a text file, an Excel spreadsheet, or the system clipboard.


Add row/column annotations from a text file, Excel file, GMT file, or the system clipboard.


Load saved Morpheus sessions or create a configuration file as described here.


Dendrograms created by external programs can be imported in Newick format.

Color Scheme

Select View > Options to edit the color scale. Typically with gene expression data, values in the heat map are mapped to colors using the minimum and maximum of each row independently. With z-scored data, categorical, or ratio data, a fixed scale should be used.

Color schemes can also be customized to easily view multiple data types.

An additional matrix can be overlayed on top of the existing matrix by opening a new matrix and selecting "Overlay onto current dataset." Data from the new matrix can be viewed with additional parameters such as size or shape by selecting conditional rendering.

Annotation Display

Right-click on a annotation header to change how an annotation is displayed. Annotations can be displayed as text, colors, or bar charts.

Calculated Annotation

Select Tools > Create Calculated Annotation to create a calculated annotation along the rows or columns. For example: Enter "MAD" for the "Annotation name". Enter "MAD()" for "Formula" and click "OK". A new row annotation named "MAD" will appear to the right of the heat map.


Rows and columns can be filtered to display a subset of the data by clicking the Tools > Filter. For numeric data, you can keep the top highest or lowest values for an annotation or a range of values.

Hierarchical Clustering

Hierarchical clustering recursively merges objects based on their pair-wise distance. Objects closest together are merged first, objects furthest apart are merged last. The result is a tree structure, referred to as a dendrogram, where the leaf nodes represent the original items and internal (higher) nodes represent the merges that occurred. Once the dendrogram is generated, a dotted line will appear that can be clicked and dragged to adjust the cut of the clusters. Gaps (white space) are introduced in the heat map between clusters that are created when cutting the dendrogram. When there are lots of singleton clusters, the width of the heat map can become too large. One way to solve this issue is by "squishing" singleton clusters together as shown here.

Type one or more search terms in the row/column search box. Blue tick marks will appear along the side or bottom scroll bar indicating where the matches in the heat map are. Hover the cursor over a tick mark to view the heat map at that data point without having to scroll. To move the matching rows/columns to the top or side of the matrix, click the "Matches To Top" button next to the search box.

New Heat Map

Slices of the selected data can be isolated from the rest of the matrix to be viewed and manipulated independently. The sliced data will appear in a new tab of the Morpheus window. Select Tools > New Heat Map to access this functionality.


The dataset can be saved as a GCT file by selected File > Save Dataset. An image can be saved as a PNG or SVG file by selecting File > Save Image. A Morpheus session which saves the current state of your view can be saved by selecting File > Save Session. Annotations or your selected dataset can also be copied from Morpheus.


Click on a column or row annotation header to sort by annotations. Shift-click to add to existing sort. Double click once along the rows/columns in the heat map to sort by the matrix values in descending order, double click twice to sort ascending, and double click three times to order the data in alternating groups of ten of most similar and dissimilar items.

Select Tools > Sort/Group to group annotations in the heat map or to lock sort levels. Groupings add whitespace to visually separate distinct values of an annotation.

Locking a sort level allows you to preserve a sort level even when other changes to sorting are made.


The matrix can be viewed with various degrees of detail by utilizing the Zoom features as well as the Fit To Window button which will allow the entire matrix to be viewed within the designated window size.

For square matrices, you can link the rows and columns so that whatever happens to the rows, happens to the columns and vice versa.


Select rows and columns in the heat map to display charts that are linked to the heat map selection by selecting Tools > Chart. Various chart types and parameters can be selected. The selected rows and columns can be changed while the chart window is open.

Nearest Neighbors

Use Nearest Neighbors to find rows/columns that are similar to rows/columns of interest.