Flapjack can import supplementary phenotype (trait) data that is associated with the genotype data set.
Importing phenotypic data¶
To import phenotype data into Flapjack, open up the
Import Data dialog and select the
Phenotypes tab where you can choose the file to import.
Phenotypes can be imported from files containing the following tab-delimited format:
# fjFile = PHENOTYPE Trait1 Trait1 Trait2 Experiment1 Experiment2 Experiment1 Line1 50 High Short Line2 2.3 High Medium Line3 99.3 Low Long
Trait data for a single trait can be either numerical or categorical. The line containing experiment information for each trait is optional.
Phenotype summary information¶
One the phenotypes are imported, Flapjack will display a summary table of the data within the
Trait Data node associated with the main data set. This is a matrix of data with lines down the left hand side and phenotypes across the top of the display. Each intersection of a line and a phenotype represents a phenotype value.
By default the phenotypes values are displayed in a heatmap format, with green representing low values and red representing high values. These colours can be changed either Flapjack wide, or for a specific trait by clicking the
Colours button on the
Phenotypic Traits tab of the
Trait Data view and selecting new colours from the
Trait Colours dialog.
Visualizing alongside genotype data¶
When you load phenotypic data into Flapjack, Flapjack selects the first three traits found in the file and displays them in a heatmap next to the main graphical genotype display. To select which phenotypes are in the heatmap, select
Data->Select traits to open the
Select Traits dialog. Select the traits you wish to display next to the lines in the genotype view, then click
Sorting by phenotype¶
Sort the lines by your phenotypic data by right clicking on a phenotype and choosing
Sort A-Z or
Sort Z-A when you have categorical data loaded, or
Sort smallest to largest’ or
Sort largest to smallest when you have numerical phenotype data loaded. You can also carry out an advanced sort by selecting
Analysis->Sort lines->By trait.
This type of sort allows you to sort by one trait first, then for lines which share values for that trait you can sort within those by a secondary trait and so on. By default the dialog will display a sinle trait to sort by and whether or not the sort will be in ascending order. You can add these secondary (tertiary, n-ary) sorts by clciking the
Add sort level button. If you decide to remove a sort level, simply click on the row you wish to remove then select
Delete sort level. Note the
Auto assign these traits to the traits heatmap once the sort is completed checkbox. If this is checked it will automatically display the traits used to carry out your sort next to the genotypes.