Roslin Bioinformatics - VIPER

User Settings and Display Options

Sections

Choosing Colour Schemes

Drop-down selection lists available in the top most menu bar of the VIPER window allow users to choose their preferred colour scheme by which VIPER highlights reported inconsistencies and missing data etc. These colours are used both in the pedigree sandwich view and the Marker and Individual Tables.

'X' menu picks the colour scheme used for reporting errors
'?' menu for reporting incomplete (and masked) data
'>' menu for highlighting individuals and their families

Error frequencies for individuals in the pedigree are actually reported as a stepwise colour map from white (no errors) through light grey, dark grey, light colour, dark colour (most red). As an aid to data exploration, by which those errors with highest error rates can be highlighted, the threshold for these colour maps can be altered using the slider control in the 'Filtered Individual Errorgram' (see Figure 1). The sensitivity colour map for Marker error reporting in the Marker Table view can not be modified.

Figure 1: Setting the Sensitivity of Error Reporting

Resizing Components

Most of the 'panels' in the VIPER frame can have their sizes adjusted, or minimized. Resizing can be done by 'grabbing' a border (with a held down mouse click) and dragging: this can be used to resize the Sandwich View / History Panel and Table Panel. The two borders between these three panels also contain minimize/restore/maximize arrows.    

The Table Panel itself contains 3 tabbed tables, the user can select which tab (table) is active ('on top') or can 'unpin' tables by dragging their tab away to a different screen area. Each table has re-sizable columns (whose order can also be changed by dragging). The data in the table can be sorted on each column by clicking on the column header.

Each of the 3 Errorgram filters can be minimized using the pan-handle control at their top left corner (see Figure 2).

Figure 2: Using Pan-Handles


The components of the Pedigree Sandwich View are resized by altering the height of each individual row in the visualisation, by grabbing and dragging the row dividers in the left-hand label column (see Figure 3). By giving different space to the different rows the size of the Individual glyphs can be optimized for clarity and to allow names and genotypes to be read. An alternative approach is to open a separate Detail View window for a family of interest (see Detail Views.)

Figure 3: Expanding Rows in the Pedigree Sandwich View

 


The separate generations of the pedigree are each collapsible using similar pan-handles to above.

Most pedigrees will contain several generations and will require the user to use the right hand scroll bar to move up and down the tree.

Ordering Parents and Offspring in the Sandwich View

In addition to being able to control the size and colours used for pedigree visualization, the user can control many further aspects of the sandwich view, to assist exploration of the data and analysis of inheritance patterns. These options are accessed by the Sandwich View menu bar (and can be hidden using the 'Hide Options' button).


The first 'Sort' menu 'Sort Within Siblings' is used to order the display of offspring in a family (Figure 4a), whilst the second is used to order the (horizontal) order of parents in the sire and dam rows of the sandwich (Figure 4b). The menus show the current precedence of attributes for ordering, items can be moved up or down the list by dragging with the mouse. The 'Sort Within a Generation' order can have a particularly profound effect on the sandwich display, dependent upon the pedigree structure. The default layout sorts first on sire names, which has the effect of grouping all of each sire's families together under one sire node: this copes well with mating strategies where a male can have multiple partners. If the reverse is true it would be better to sort first on dam name. However, if both sires and dams have multiple partners there is no ideal solution and the layout automatically draws duplicate nodes for some parents so that the correct parent pairs can be made. Any such duplicate nodes are linked by grey arcs. Choosing to sort on attributes other than name can have the effect of introducing many duplicate nodes to generate the desired ordering, but can be useful to group families with high error rates etc.

Figure 4: Sort Menus


The 'Families' menu is used to select whether the offspring of a family are shown grouped together as a single family icon, or whether the individual offspring are rendered with their own icons ('Individual Error Display'). For the family view it is possible to choose whether the metrics used reflect the average or maximal values of offspring in the family('Average Offspring Error' versus 'Max Offspring Error').

The final 'Split Offspring' menu allows the user to split the offspring (or sub-families for the family view) into separate rows. The options currently are to split rows according to:

  • No Split
  • By Gender divides offspring into Male, Unknown, Female rows
  • Has Offspring divides offspring into Reproducing or Dead End rows
  • Masked divides offspring that have been masked for any genotype into a separate row
  • Removed Parent Links divides offspring according to whether the user has broken sire or dam links

Note currently some of these views do not immediately update properly when an individual is moved to different row, for example following masking. Updating can be forced by toggling to a different split view and then back.

Detail Views

Two separate detailed views of a selected family can be created, which open in new windows. These are selected via the left mouse click window on an individual or family in the pedigree (Figure 5). Both detail views can be captured as screenshots (see Saving Data)

Figure 5: Left-Mouse-Click Context Menu.


The first detail view is simply an expanded sandwich view of the family in isolation, which is again re-sizable (Figure 6).

Figure 6: Detail View Window


The

view options are inherited from the parent window, e.g. the sorting and partitioning of offspring. The mouse hover window will also open to display the error metrics over each node (See Figure 7).


The 'Pedigree Chart View' presents a node-link graph view of the family, where each offspring is linked to both parents (Figure 7). This view can only be activated for families that have already been 'selected' (i.e. highlighted using the context menu). The size of the selection can be expanded to include more ancestors, descendants and half-siblings etc. generating increasingly complicated views (see Figure 8).

Figure 7: Pedigree Chart View Window

Note the mouse hover window displaying the error metrics for B853. The view is re-scalable, and the user can split parents by sex (male G707 above here, female G558 below). The same colour maps are used for reporting errors and data incompleteness, and here inconsistent child-parent relationships are directly coloured.

Figure 8: Pedigree Chart View Window for wider family groups

The upper panel shows the parent generation split on sex as in Figure 7, whilst the lower panel presents a more traditional hierarchical view of the pedigree.