QTL Viewer

WARRANTY DISCLAIMER AND COPYRIGHT NOTICE

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version."

Dependencies:

• Mousemap library for converting between cM and bp.
• SimpleOpenNI for Kinect interaction.

Standard version:

Usage

Click a tab to change to that page.

• File manager:
  • Go to File>Open to load a file or folder. The file(s) will appear in the side bar as a header with a list of phenotypes.
  • To activate a phenotype, check the square to the left of the label.
  • To change the color of a phenotype, click the colored rectangle to the left of the label. A color selection box will appear.
  • To show or hide a file's contents, click the appropriate symbol to the left of the file name.
  • To remove a file or phenotype from the list, click the "X" symbol to the right of the name. The "X" will not appear until the cursor is over the name.
  • To hide the file manager bar, click anywhere between it and the tab pages.
• LOD score plot:
  • Zoom in/out or reset with the appropriate options under the View menu option, or by holding command/control and scrolling the mouse wheel.
  • Scroll through the graph with the mouse wheel, or by clicking and dragging.
  • View an individual chromosome by clicking it.
  • Return to the genome-wide view with View>Show All, or by scrolling the mouse wheel quickly up.
  • Switch to the next or previous chromosome with the View menu.
• Chromosome view:
  • Click a chromosome to view it in the LOD score plot.
• Menu:
  • Click the menu tab at the bottom of the screen or use the View options to show/hide the menu.
  • Use the text boxes to change the default LOD thresholds.
  • Use the centimorgans and base pairs radio options to change the units.
  • Click the "Load config" button or use the File menu options to load a new configuration file.

Kinect version:

Installation

Requires SimpleOpenNI wrapper for Processing. See http://code.google.com/p/simple-openni/wiki/Installation.

Setup

Stand about 10 feet from the Kinect sensor. On the right side of the screen there is a camera display; make sure that all limbs are visible. To calibrate, hold both hands at head level with shoulders and elbows making right angles.

Interaction

• Use right hand to control the cursor (a red circle).
  • The cursor becomes more sensitive to movement as hand gets closer to the sensor.
  • If hand drops below the threshold of sensitivity, the cursor will become translucent.
  • To select an item, keep hand in the same position for two seconds. A blue circle will begin to wrap around the circle, activating after a full revolution. Activation will fail if the cursor is moved. After activation, the cursor will have to be moved again to allow another action.
• Use left hand to pan vertically and horizontally.
  • A black arrow will appear to indicate direction.
  • Vertical panning is used in the file browser and phenotype list to switch between pages of a folder list/file.
  • Horizontal panning is used in the phenotype selector to switch between files, and in the LOD score plot to move across when zoomed in.
  • In addition, panning quickly down in the LOD score plot will reset the pan and zoom.
• Use both hands to zoom.
  • This action is similar to using a multi-touch device: move hands together to zoom out, and apart to zoom in.
  • Keep hands in the same positions until the indication bar disappears to end zooming.
• Hold left hand at an angle to use secondary selection.
  • A green progress meter will appear, and will activate after 2.5 seconds. Move left hand out of the required angle to stop activation.
  • The cursor can be moved during activation.
  • After activation, move left hand to allow another action.

Usage

Select a tab to change to that page.

• File browser:
  • Select a folder to browse its contents, or a file to load it.
  • Use left hand to scroll up and down.
  • The name of the current directory is shown at the top on the right.
  • Select one of the folders in the complete path shown at the top to change directly.
• Phenotype list:
  • Select a phenotype to change its color. Select outside of the box to end color selection.
  • Use secondary selection to choose a phenotype for display.
  • Select the file name at the top to remove it from the list.
  • Use left hand to scroll vertically through pages, and horizontally through files.
• LOD score plot:
  • Zoom in with both hands, and scroll with left hand.
  • Select a chromosome to view it individually.
  • Scroll quickly down to reset pan and zoom.
• Chromosome view:
  • Select a chromosome to view its LOD plot.
• Settings page:
  • Select the +/- buttons to change the default LOD thresholds.
  • Select the centimorgans or base pairs radio options to change units.
  • Select the "Stop tracking" button to stop using the program.
  • Select the "Exit" button to be prompted for closing the program.

How to switch versions:

Change the boolean field ENABLE_KINECT on line 31 to true for Kinect interaction, or false for the regular application.