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.
Acessions 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 be further used 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 acessions shown at the top will display "Filtered" together with the number of acessions that match the filter. This will also update the sample selction 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¶
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.
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