Description: A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data
Author: Joshua Gould, The Broad Institute
The HeatMapViewer displays values in a heat map format where by default the largest values are displayed as the reddest (hot), the smallest values are displayed as the bluest (cool), and intermediate values are a lighter color of either blue or red. This is a very convenient way to display three-dimensional data (samples, features, and values).
There are a number of options controlling the appearance of the heat map that can be set by selecting View>View Options:
Users can save the heat map image to a file by selecting File>Save Image. Supported formats are bmp, eps, jpeg, png, and tiff.
You can use the viewer to create a new dataset.
Feature labels use color to annotate features in the heat map.
To use feature labels:
The feature annotations legend can be saved to a file by selecting File>Save Feature Labels Legend.
Sample labels use color to annotate samples in the heat map.
To use sample labels:
The sample annotations legend can be saved to a file by selecting File>Save Sample Labels Legend.
GeneCruiser retrieves information about Affymetrix probe identifiers and adds the information to the feature table.
To use GeneCruiser annotations:
You can also load descriptions from a csv (comma separated values) file. To load descriptions from a csv file, select File>Load Descriptions From Csv File.
To find a feature in the heat map, select Edit>Find. You can choose whether to match the case of the text you’re searching for by selecting the Match case checkbox at the bottom of the find dialog. You can also choose whether to include the description column in your search by selecting the Include Descriptions In Search checkbox.
The expression profile for a feature plots expression value per sample.
To display an expression profile:
The centroid plot shows the mean expression value for each sample. The error bars represent the standard deviation.
To display a centroid plot:
The histogram plot shows the distributions of expression values. The vertical axis represents number of occurrences. The horizontal axis represents the binned expression values.
To display a histogram:
The nearest neighbors item shows other features whose expression values follow similar trends to the selected feature. There are four choices for the distance metric: Cosine, Euclidean, Manhattan, and Pearson.
To display the nearest neighbors:
The scatter plot lets you compare expression values in two samples.
To display a scatter plot:
The sort features item lets you order features in the heat map by differential expression based on either T-Test or Signal To Noise calculations. To sort features:
The sort samples item lets you order samples in the heat map by class. To sort samples:
You can use your keyboard to quickly accomplish many tasks. To find the shortcuts for common commands, look in the menus or select Help>Keyboard Shortcuts to see a list of available shortcuts.
|dataset *||The dataset to display - .gct, .res, .odf|
* - required
|11||2013-06-21||Fixes Java 7 launching issues.|
|10||2010-08-04||Fixed bug with incorrect scores listed for features in the Nearest Neighbors table|
|9||2010-03-18||Fixed bug in calculating standard deviation for centroid plot.|
|8||2007-09-05||Fixed bug in color scheme legend dialog. Added gene neighbors analysis.|
|6||2007-08-13||Additional additional plots, keyboard shortcuts, and ability to label samples from sample info file.|
|5||2006-10-05||Plot selected samples only in profile plot|
|4||2006-09-25||Added eps output file format|
|3||2006-08-08||Save row names with image|
|2||2005-06-07||Annotated for GP 1.4.|