HeatMapViewer Documentation, v11  Print-icon ▸ Open Module on GenePattern Public Server

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

Contact: gp-help@broadinstitute.org

Summary

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).

Display Options

There are a number of options controlling the appearance of the heat map that can be set by selecting View>View Options

Saving Images

Users can save the heat map image to a file by selecting File>Save Image. Supported formats are bmp, eps, jpeg, png, and tiff.

Saving Datasets

You can use the viewer to create a new dataset.

  1. Select File>Save Dataset. A window appears.
  2. Choose the features and samples to include in the dataset by selecting the features and sample names in the viewer.
  3. Choose a location and name for the new dataset.
  4. Click Save to save the new dataset. 

Feature Labels

Feature labels use color to annotate features in the heat map.
To use feature labels:

  1. Create a grp, gmx, or gmt file. A complete description of these formats is available on the GenePattern website.
  2. Select File>Label Features to open your feature set file. You have the option to restrict the view to features in your feature set. To return to the full view, select View>Reset Dataset. A color bar appears next to each feature in the feature set in the table.
  3. Select Edit>Feature Labels to edit the color or close the feature set.
  4. In the Feature Labels window, select your feature set from the drop-down list. The color assigned to that feature list appears in the box to the right.
    • To change the color, click the box and select a new color.
    • To delete the feature set and remove the color bars from the table, click Delete.

The feature annotations legend can be saved to a file by selecting File>Save Feature Labels Legend.

Sample Labels

Sample labels use color to annotate samples in the heat map.
To use sample labels:

  1. Create a cls file or sample info file. A complete description of these formats is available on the GenePattern website
  2. Select File>Label Samples to open your cls or sample info file. A color bar appears below each sample name.
  3. Select Edit>Sample Labels to edit the color or close the sample info file.
  4. In the Sample Labels window, select your sample class from the drop-down list. The color assigned to that sample class appears in the box to the right.
    • To change the color, click the box and select a new color.
    • To delete the sample class and remove the color bars from the table, click Delete.

The sample annotations legend can be saved to a file by selecting File>Save Sample Labels Legend.

Loading Descriptions

GeneCruiser retrieves information about Affymetrix probe identifiers and adds the information to the feature table.
To use GeneCruiser annotations:

  1. Select File>GeneCruiser.
  2. Select the features that you want to retrieve annotations for in the table.
  3. Choose which fields to retrieve from GeneCruiser in the GeneCruiser dialog.
  4. The annotations appear in additional columns in the table.

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.

Finding Features

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.

Profile Plot

The expression profile for a feature plots expression value per sample.
To display an expression profile:

  1. Select one or more features and optionally select one or more samples.
  2. Click View>Profile. Alternatively, right-click and select Profile from the context menu or click the profile plot column in the feature table.

Centroid Plot

The centroid plot shows the mean expression value for each sample. The error bars represent the standard deviation.
To display a centroid plot:

  1. Select two or more features and optionally select one or more samples.
  2. Click View>Centroid Plot. Alternatively, right-click and select Centroid Plot from the context menu.

Histogram

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:

  1. Select one or more features and optionally select one or more samples.
  2. Click View>Histogram. Alternatively, right-click and select Histogram from the context menu.

Nearest Neighbors

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:

  1. Select one feature.
  2. Click View>Nearest Neighbors. Alternatively, right-click and select Nearest Neighbors from the context menu.

Scatter Plot

The scatter plot lets you compare expression values in two samples.
To display a scatter plot:

  1. Select two samples.
  2. Optionally select one or more features.
  3. Click View>Scatter Plot. Alternatively, right-click and select Scatter Plot from the context menu.

Sorting Features

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:

  1. Label features as described in the Label Features section (if you have not already done so).
  2. Select View>Sort Features.
  3. Select the feature label to use for sorting, the test statistic to use, and whether to sort in ascending or descending order.
  4. To return to the original order, select View>Reset Dataset.

Sorting Samples

The sort samples item lets you order samples in the heat map by class. To sort samples:

  1. Label samples as described in the Label Samples section (if you have not already done so).
  2. Select View>Sort Samples.
  3. Select the sample label to use for sorting.
  4. To return to the original order, select View>Reset Dataset.

Keyboard Shortcuts

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.

Parameters

Name Description
dataset * The dataset to display - .gct, .res, .odf

* - required

Platform Dependencies

Module Type: Visualizer
CPU Type: any
OS: any
Language: Java

GenePattern Module Version Notes

VersionRelease DateDescription
112013-06-21Fixes Java 7 launching issues.
102010-08-04Fixed bug with incorrect scores listed for features in the Nearest Neighbors table
92010-03-18Fixed bug in calculating standard deviation for centroid plot.
82007-09-05Fixed bug in color scheme legend dialog. Added gene neighbors analysis.
62007-08-13Additional additional plots, keyboard shortcuts, and ability to label samples from sample info file.
52006-10-05Plot selected samples only in profile plot
42006-09-25Added eps output file format
32006-08-08Save row names with image
22005-06-07Annotated for GP 1.4.
12004-12-22