Views the results from ComparativeMarkerSelection
Author: Marc-Danie Nazaire (The Broad Institute), Thorin Tabor (University of California San Diego, The Broad Institute)
The ComparativeMarkerSelectionViewer provides tools for reviewing and working with ComparativeMarkerSelection results. These tools include plots, a data table, expression profiles, filters, and creating dataset and feature list files. (A feature list is a text file with one feature per line.)
ComparativeMarkerSelectionViewer is an interactive tool. For non-interactive access to annotations, heatmaps, and creation of datasets and features lists, see the HeatMapImage, and ExtractComparativeMarkerSelection modules.
Heatmap and plots are displayed in the upper portion of the viewer. Use the View menu to select the plot to display:
Use the mouse to click-and-drag over the plot area to zoom in.
Use the Reset button (upper right of plot) to return the zoom to the default level.
Note: Zoom in/out not available for heatmap.
The table in the lower portion of the viewer lists the ComparativeMarkerSelection results. For a description of each column, see the ComparativeMarkerSelection documentation. By default, the features in the table are ordered by score. To reorder the features, click the title of the key column; for example, to order features by rank, click Rank.
To choose which columns are shown in the table, click the Column Show/Hide toggle icon in the top-left corner of the table, just to the left of the search bar:
Using File>Save Table, you can export the table in tab delimited format for use in external programs such as Excel. This will result in a tab-delimited file with the contents of the table, leaving out any items excluded due to filters or columns hidden through the Column Show/Hide toggle.
The expression profile for a feature plots expression value per sample. A heatmap shows the same information, but color codes the expression values from red for the highest expression values through blue for lowest expression values.
To display an expression profile:
Use filters to display only features that you are interested in:
You can use the viewer to create a new dataset in GCT format or a feature list (a text file with one feature per line) containing a listing of the selected features in the table in from the ComparativeMarkerSelection results:
Gould et al. Comparative Gene Marker Selection suite. Bioinformatics Advance Access published on May 18, 2006, DOI 10.1093/bioinformatics/btl196.
|comparative marker selection filename *||The output from ComparativeMarkerSelection|
|dataset filename *||The dataset file used as input to ComparativeMarkerSelection|
* - required
|9||2017-09-15||Update to fix data table in upregulated graph, when used in the GenePattern Notebook env|
|8||2016-06-06||New Java Script module - replaces previous Java Applet visualizer|
|7||2015-03-17||Fix for SecurityException when saving datasets|
|6||2014-07-28||Added filter by multiple criteria, hide table columns, export table. Fixed for use with Java 7. Many other improvements and bug fixes.|
|5||2013-09-20||Added filter by rank, filter by multiple criteria, hide table columns, export table. Fixed for use with Java 7. Many other improvements and bug fixes.|
|4||2006-07-29||Updated GeneCruiser library|
|3||2006-03-09||Updated to work with latest ComparativeMarkerSelection module|
|2||2005-06-13||Added maxT p-value and removed rank p-value|