Select File > Open to import data.
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.
Right-click on a annotation header to change how an annotation is displayed. Annotations can be displayed as text, colors, or bar charts.
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()"
"Formula" and click "OK". A new row annotation named "MAD" will appear to the right
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 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
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.
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
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
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.
Use Nearest Neighbors to find rows/columns that are similar to rows/columns of interest.