Information & Computational Sciences

• Flapjack Homepage

• Welcome to Flapjack Help
• Quickstart
• Projects and Data Formats
• Genotype Visualization
• Chromosome Map Scaling
• Bookmarks
• Modes and Views
• Selecting Lines/Markers
• Exporting Data
• Colour Schemes
• Phenotype Visualization
• QTL Visualization
• Graph Visualization
• Command Line Support

• File
• Edit
• View
• Visualization
• Data
• Help

• Import Data Options
• Import Data
• Duplicate Markers
• Show/Hide Markers
• Show/Hide Lines
• Export Image
• Export Data
• Customize Colours
• Select Traits
• Create New View
• Toggle Visible Displays
• Sort Lines: By Similarity
• Sort Lines: By Trait
• Sort Lines: Importing Order
• Filter QTLs
• Find By Name
• Allele Frequency Threshold
• Database Link Settings
• Preferences

• What's New
• Flapjack Tips

Flapjack Tips

Hints and tips on how to use Flalpjack are shown periodically in its status bar running along the bottom edge of its main window. For easy reference, the following is a list of all the tips that may appear:

• Hold CTRL while clicking and dragging lines or markers to move them to new positions

• You can import and work with multiple data sets at once, all within a single project

• Many of Flapjack's menu options are also accessible by right-clicking on the display canvas

• Compress projects to save disk space by selecting the option in the Preferences Dialog

• The ordering of lines is common across all chromosomes within a view

• The Overview Dialog (F7) displays the entire data set, scaled to fit any window size

• Navigate around a view quickly by clicking and dragging on one of the Overview displays

• Flapjack will periodically check for new versions at startup

• The red rectangle on an Overview display shows the region of the data set currently being viewed on the main canvas

• Mouse over any allele position to view further information on it

• Toggle the overlaying of actual genotype data onto the canvas by pressing CTRL+G

• You can search for lines or markers by name by using the Find Dialog (CTRL+F)

• Search for all lines beginning with the letter 'A' by using the Find Dialog's regular expression: A.*

• You can move the canvas's viewpoint around by simply clicking on it and dragging with the mouse

• Zoom in or out by using the slider, or by holding CTRL and scrolling the mousewheel

• Create multiple custom views of the same data set by selecting 'Visualization->Create new view' from the menu bar

• Please send any comments, feature requests, bug reports, etc, to flapjack@germinate.org.uk

• Customize the various colour schemes by selecting the 'Customize' option from within the 'Colour schemes' sub-menu

• Show or hide the various Flapjack displays using the 'Toggle visible displays' menu option

• Quickly hide individual lines or markers by CTRL double clicking on them (while line or marker mode is active)

• Switch to 'marker mode' to select, deselect, or toggle marker visibility

• Switch to 'line mode' to select, deselect, or toggle line visibility

• Quickly track locations of interest by right-clicking on the display and selecting 'Bookmark location'

• Move QTLs between tracks by holding CTRL and dragging them with the mouse

• Change which QTLs are visible by selecting Data->Filter QTLs from the menu bar

JHI Plant Bioinformatics Group