Genotype tab¶
Genotype data is visualised in the Genotype tab in the right hand panel
The genotype matrix requires two inputs, the features and accessions which can be inputted a number of ways.
Inputting features and accessions¶
Note
The accessions can only be added once a VCF file has been added to the view. Searching for a dataset
Features can be selected via the view by selecting a region of the axis.
Accessions can be added via a pop out menu from the genotype tab.
If the exact feature names are known, it can be inputted using the VCF Genotype Search function
Interpreting the genotype matrix¶
| Display | Meaning | Colour |
|---|---|---|
| 0 | Reference | Blue |
| 1 | Heterozygous | Light-blue |
| 2 | Alternate | Orange |
Selecting a haplotype and ordering the genotype matrix¶
The cells located in the ref and alt columns can be clicked on to select a specific haplotype. The selected haplotype can be further used to filter a VCF for a given haplotype. When selected, the genotype matrix will be ordered based on the specific haplotype pattern.
Filtering by a defined haplotype¶
If a haplotype is selected by clicking the cells in the ref and alt columns, the loaded VCF file can be searched using the selected haplotype.
When checked, text will appear below the check box to indicate that the VCF is being searched.
Afterwards the number of accessions shown at the top will display "Filtered" together with the number of accessions that match the filter. This will also update the sample selection box to ONLY include those that match the given haplotype pattern.
Note that the search will also return HET (1) results. If you wish to filter them out, please check the "Match exact alleles" button.
Accessing passport data for selected samples¶
Viewing passport data in genolink¶
To access the passport data for the selected samples, simply just click on the Genolink button. This can be useful after filtering for a defined haplotype.
Viewing passport data in the genotype table¶
New feature in v3.9.0
Genotype data can now be viewed in the genotype table.
In the actions sub menu in genotype tab press the "Select Passport Fields" to select the fields to add.
To select multiple fields you can hold shift and click two points to select a range or hold the ctrl to select individual points.
To resize the passport fields click and drag on the below icon on the left hand side of genotype matrix table.
To reorder the passport click and drag the fields up and down.
To view the individual passport data without resizing the fields, mouse over the cell and the field will appear.
Genotype table display options¶
Resizing the genotype matrix¶
The genotype matrix can be resized by dragging the right hand side of the genotype tab.
And its headings can be resized using the slider in the table headings
Genotype matrix alternative colour theme¶
To select an alternative colour scheme, go into the Genotype accession selection menu, click on the controls tab and click on the Choose Colour Theme button