Phenotype Visualization¶
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 OK
.
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.