Roslin Bioinformatics - VIPER

The VIPER Interface

Moving your mouse over the image below will show descriptions of the various components. Click on an area to got to a fuller description.

Application Menu Bar Information Panel: files loaded, counts of individuals, markers, genotypes and errors Filter control to mask markers above a given error threshold Tick box controls to couple/decouple redrawing with slider action Filter control to mask markers below a given error threshold Filter control of colourmap thresholds for reporting errors on individuals History Panel: navigable branched hierarchy of selectable checkpoints of changes applied to the data Tabs to choose which Table is displayed ontop (or to unpin a table by dragging) Button to revert from single marker to aggregate view (inactive here) Marker Table: sortable columns detail error and incompleteness counts for each marker etc. (White-Grey-Colour map  reflects error frequency) Cheat button to mask all remaining inconsitencies Button to call inheritance algorithm, recalculate pedigree metrics and redraw the data. (Inactive here). Button to revert recent maskings that have not yet been recalculated/checkpointed. Sandwich Menu Bar: controls for various display options Generation1: Title Bar for rows in the sandwich: borders act as resizable handles to rescale the rows of the sandwich Second Generation in the pedigree Scrollbar to navigate up and down the generation hierarchy of the pedigree Generation1: Sires in founder generation Generation1: Dams in founder generation Generation1: Offspring of sire B1205 and 4 different dams (i.e. 4 families) Generation1: Offspring of sire B1212 and 3 different dams (i.e. 3 families) Generation1: Offspring of sire G323 and 2 different dams (i.e. 2 families) Generation1: Offspring of sire G383 and 3 different dams (i.e. 3 families) Secret Wormhole

Menu Bar
The main VIPER menu controls data loading, the saving of cleaned data and screenshots and user colour options. The 'Help' button links to the VIPER help documentation online.

Information Panel
The Information Panel details the data files loaded and the totals of individuals, markers and genotypes parsed from these files.

Errorgram Filters
Master Marker Errorgram
A slider controlled filter for removing high error-rate markers from the dataset (see full description)

Filtered Marker Errorgram
A slider controlled filter for (temporarily) masking low error-rate markers (see full description)

Filtered Individual Errorgram
A slider to control for the colour sensitivity of error reporting on individuals and families in the Sandwich View and Individual Table (see full description)

Synchronize Filters Selection Boxes
Checkboxes to decouple immediate reapplication of the inheritance algorithm as the sliders are moved. Beneficial for larger datsets (see full description)

Pedigree Sandwich View
VIPER uses a novel visualisation to represent the pedigree hierarchy as a set of stacked generation sandwiches. Each generation sandwiches offspring between sire and dams, creating families with shared parents. (see Sandwich View for more detail).
Sandwich View Menu Bar
Controls for various visualisation options for the Sandwich View, for example toggling between Family versus Individual Views (see Sandwich View) and controlling how the Individuals are ordered in the layout (see full description of menu).

Sandwich Title Bar
Labels for the sire, dam and offspring rows in the visualisation. Used for resizing the components for readability etc. (see full description of resizing).

Generations
Each parent/offspring generation in the pedigree is represented by a collapsible and re-sizable 'Sandwich'. Generations stack on top of each other in a hierarchy that if necessary can be navigated up and down by scrollbar. Each sandwich is composed of rows of sires (i.e. male parents) and dams (female parents) sandwiching the offspring (family) of a mate pair.
 
Masking Suspect Data
Various controls allow suspect data points (markers, genotypes, individuals and pedigree relationships) to be masked (described in more detail). After performing 'Mask' operations the 'Recalculate Errors' button is used to initiate revalidation of the dataset with the inheritance checking algorithm. The 'Undo Recent Maskings' button can undo the current group of masked data points, whilst the 'Mask Remaining Errors' button can be used to mask all remaining genotypes reported as in error.

Tabulated Data
Three tables are displayed in a single tabbed-pane. These display all of the reported errors, genotype incompleteness and maskings applied for each Marker and Individual. The data displayed in each table can be sorted by clicking on the column headers, allowing the data to be reorganized by any of the reported inheritance and genotype metrics. Using the the Marker Table it is possible to select individual markers for masking, and to toggle the pedigree view between reporting aggregate results across all markers or reporting the detail for a single selected marker. Single marker focus is reverted to the aggregate view with the button 'Clear Focus Marker'. (See Masking Markers for more detail).

History Panel
Each time data is masked and the inheritance inconsistencies recalculated, a checkpoint is taken on the data and displayed in the history panel. The user can then revert to one of these data states and perform a separate analysis (creating a branched history tree) (see example in Figure 2).