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

Visualization Menu

This reference page describes each item found within the Visualization menu of Flapjack's main menu bar.

Export view as image

Displays the Export Image dialog that allows you to save various captures of Flapjack's display area to disk.

Export view as image

Displays the Export Data dialog that allows you to save the state of the current data set (maps, markers, and genotypes) as plain text files.

Colour scheme

Opens a sub-menu displaying various options for selecting or modifying the colour scheme in use by the current view.

Nucleotide model

Selects the nucleotide model as the current colour scheme for the view.

Simple 2 colour model

Selects the simple 2 colour model as the current colour scheme for the view.

By similarity to line (2 colour)

Prompts for a comparison line and uses it as the basis for setting the line similarity scheme as the current colour scheme for the view.

By allele frequency

Selects the allele frequency colour model as the current colour scheme for the view, and displays the Allele Frequency Threshold dialog to confirm its settings.

Random (HSB)

Selects a random colour model (based on hue/saturation/brightness values) as the current colour scheme for the view.

Random (Websafe)

Selects a random colour model (based on a palette of 216 web safe colours) as the current colour scheme for the view.

Customize

Displays the Customize Colours dialog that allows you to select and/or modify the colour scheme for the current view in more detail.

Overlay genotypes

Toggles on or off the option to display textual genotypic information as an overlay on top of each visible allele position. Regardless of this setting's state, it will only take effect at higher zoom levels (when the size of each allele's "box" is large).

Highlight heterozygotes

Toggles on or off the option to enhance the display of heterozygous alleles, dimming all other remaining alleles so that they are less visible.

Highlight gaps

Toggles on or off the option to enhance the display of missing data, dimming all other remaining alleles so that they are less visible.

Select traits

Displays the Select Traits dialog that allows you to pick which traits should be displayed on the traits heatmap alongside the list of line names.

JHI Plant Bioinformatics Group