VlaaiVis Online Reference Guide

VlaaiVis - Online Reference Guide

Purpose and Principle

1. Menu and Toolbar
2. Details
3. Main Window
4. Zoom and Barchart
5. Data Details
6. Legend

Configuration Designer

Purpose and Principle

The Pie BarChart displays the profile of a compound. When used for an entire dataset, it allows for an easy checkup on the completeness and correctness of the data, and comparison of compounds. Pie Barchart visualization can be customized by indicating a preferred (wanted) profile in the dedicated Configuration tool, accessible by choosing Tools > Configuration from the main menu

The Preferred Profile determines the Properties (columns) of your dataset, groups them into colored Segments and defines the range a Property should reside in to be considered "good". A Pie Barchart visualization represents the Preferred Profile as the outer rim of the Pie Barchart (the gray zone), and each Property as a colored wedge in the circle.
Typically, at the early stages there'll be a lot of Compounds with a small number of Properties, while later in the project, this will be the inverse. As such, the Preferred Profile can change over time.

To interpret a Pie BarChart, follow this simple rule: THE FULLER THE BETTER.

Example

The below Pie Barchart has all its RED wedges near the edge and inside the gray outer rim (and thus inside the Preferred Profile range for RED), resulting in quite a full RED segment.

The GREEN segment's first 8 wedges (counting clockwise) are alright too, although the 3rd GREEN wedge is showing an error. The last 3 GREEN wedges are near the origin of the circle, almost as far as they can be from the preferred range (either much too high or much too low).

The GREY segment is reasonably OK, with only the 8th wedge slightly outside the Preferred Profile range (and the 4th just touching it). The narrower width of the wedges in the GREY segment hints at the relatively low importance of these properties with respect to the other wedges.

LIGHTBLUE is more dispersed, as some wedges seem very good while others are near the origin of the pie and thus far off of the Preferred Profile range for LIGHTBLUE.

DARK BLUE values are perfect for the 2 wedges that are filled, but the white wedges indicate there's 2 DARK BLUE properties that haven't been measured yet (or at least lack the data in the dataset).

To see the value range and Preferred Profile limits for each of the wedges, move and hold mouse cursor over a wedge. A yellow tooltip window providing this information will be displayed.

Representation

The value of a Property in respect to the range for that Property set in the Preferred Profile is shown by coloring a proportional part of the wedge. Note that you cannot determine the absolute value of a Property from this representation: it only shows if the Property hits the target set in the Preferred Profile or not (i.e. when the wedge extends into the gray zone, it's a hit). In case of a miss, it doesn't show if it's over or under target. The neared to the origin, the more you missed the target by.

Score (aka Percentage Filled)

The number in the lower right-hand corner represents how much of the Pie BarChart surface is filled (and thus how much it approximates the Preferred Profile). Score is calculated on the currently visible elements of a Pie BarChart, and as such changes when you hide / show columns (here or in the Details window) or segments (in the Legend window). Empty columns (zeroes) as well as missing data (NULL values) all contribute to the percentage filled. As such, compounds with a lot of missing data will rank very low on Percentage Filled although they might prove to be the better compounds later. Consider it a trigger to go and fetch more data if you're doubting the Percentage Filled score for certain compounds. An alternative would be to Hide the PieSlices you're typically missing data for, to get a calculated Percentage Filled without their contribution.

Note: Percentage Filled is no longer shown when the pies are too small to read the text. Try zooming in.

1. Menu and Toolbar

File / Import to open a file

Allowed file formats

TXT file (tab delimited text file)

CSV file (comma delimited text file)

SD file

File / Export to export (save) a file

Allowed file formats

to TXT file (tab delimited text file)

to CSV file (comma delimited text file)

to SD file (needs to access the webservices at J&J Beerse to do a conversion from SMILES to MOLSTRUCT)

to SMILES (SMILES file)

View to select visible windows

Legend

Zoom

Details

Data Details

Barchart

View / Mode to select different viewing modes

Show Scale (F2)
shows the scale for each PieSlice.
Note if the PieBarChart is too small to show a meanigful scale, the drawing is omitted. Try zooming in.

Show Preferred (F3)
shows the preferred range for each PieBarChart in overlaid gray.

View / Save Layout and View / Load Layout

Save (load) the current window layout to (from) disk.

Follow to set how the other windows will follow the data shown in the main window

Hover
Windows show the details for the PieBarChart / PieSlice the mousepointer is hovering over (follow mousepointer)

Click
Windows show the details for the PieBarChart / PieSlice the user last clicked on (follow mouseclick)

2. Details

Shows the actual data set, including columns that are not shown in the PieBarCharts. Columns are grouped and coloured according to the segments defined for the PieBarCharts.
Columns that are configured to be part of the PieBarChart, but are hidden by the user (either from the Legend or from the right-click context menu) will have gray text.

Data interpretation

VlaaiVis is capable of differentiating between text and numbers and will sort them alphabeticaly or numerically. In addition, dates are recognized as well (and can also be used for sorting and filtering) if they're in one of these formats:

Format Examples

dd/MMM/yyyy
- one or two digits for the day
- short name (three characters) for the month
- four digits to represent the era and year
The parts are separated by slashes.
1/Dec/2005
01/JAN/2006

dd/M/yyyy

- one or two digits for the day
- one or two digits for the month
- four digits to represent the era and year
The parts are separated by slashes.

1/12/2005
01/1/2006

Sorting

Click on a column header to sort ascending on that column, click again for descending. The sort order is indicated by an upward or downward arrow in the columnheader.

Filtering

Use the dropdowns to filter on a specific column to filter on values for that specific column, this works more or less like the filtering function in Excel.

By selecting 4.85 in this case, only compounds for which the hENT1_pIC50_ADO_TrPain value is equal to the 4.85 are kept:

To remove the filter criterion for a single column you can just select (none) from the dropdown list and the filter for that column will be removed. You can clear the filter criteria for all columns at once by clicking the icon on the top-left of the Details window.

For more advanced filtering you can use the (custom) item from the filtering dropdown. This opens the Custom Row Filter window in which you can specify more advanced filtering criteria, as shown below.

Format	Examples
dd/MMM/yyyy	- one or two digits for the day - short name (three characters) for the month - four digits to represent the era and year The parts are separated by slashes.	1/Dec/2005 01/JAN/2006
dd/M/yyyy	- one or two digits for the day - one or two digits for the month - four digits to represent the era and year The parts are separated by slashes.	1/12/2005 01/1/2006

3. Main Window

Selecting

All other windows follow either the last clicked PieBarChart / PieSlice, or the one your mousepointer is hovering over, depending on the Follow setting on the Toolbar.

Click to select a PieBarChart

Shift-Click to select a range

Ctrl-Click to select multiples

Browsing

Scroll to browse through the PieBarCharts (also PgUp / PgDn)

Zooming

Ctrl-MousewheelScroll or Ctrl-minus / Ctrl-plus to zoom in and out

Sorting

Right-Click on a PieBarChart
sort on Percentage Filled (ascending or descending)

Right-Click on a PieSlice
sort on this PieSlice (ascending or descending on value or slice percentage filled)

Show / Hide columns in PieBarChart

Right-Click on a PieSlice and select Hide / Show that column in the PieBarChart.

Copy to Clipboard

Right-Click on a PieBarChart and select Copy chart to Clipboard. You can then paste (CTRL-V) it in any other application as an image (no longer interactive)

4. Zoom and Barchart

The Zoom window shows a single PieBarChart, either the last clicked PieBarChart, or the one your mousepointer is hovering over, depending on the Follow setting on the Toolbar.

The BarChart window shows a BarDiagram for each currently visible PieSlice (absolute value). Preferred Range is shown as well, if it is selected in the View / Mode Menu.

5. Data Details

Shows the details of either the last clicked PieSlice, or the one your mousepointer is hovering over, depending on the Follow setting on the Toolbar. The graphical BarDiagram representation is the same as is used for all PieSlices in the BarChart window.

Value the actual value (from the imported dataset) for this PieSlice

Minimum the minimum value for the entire range of values for this PieSlice

Pref. Minimum the preferred minimum the value should be to fall into the preferred range

Pref. Value the exact value of the very edge. Usually this is the mathematical middle of Pref. Minimum and Pref. Maximum.

Pref. Maximum the preferred minimum the value should be to fall into the preferred range

Maximum the maximum value for the entire range of values for this PieSlice

Flipped Either False or True. When Flipped, a PieSlice range is flipped (the scale is inverted and goes from Maximum to Minimum)

6. Legend

Shows the colours of the segments and their interpretation.

Hide / Show Segments

Click on a colour to Hide / Show the specific segment. Hidden segments have their text shown in grey, visible segments in black

Designer

To edit the Preferred Profile, choose Tools > Configuration from the main menu. The Designer lets the user add, delete and update the properties and target ranges making up the Pie Barchart.

Drag and drop a column (or multiple columns) from the left pane to the correct segment (as indicated by the color) in the right pane to add them to the Pie Barchart definition. Then fill out the boxes to set the expected value range and Preferred Profile. Drag and drop columns between segments to change their position.

Use the Load and Save buttons in the lower left corner to import / export Pie Barchart configuration files.
Note: these configuration files are mutually compatible with the configuration files used in Third Dimension Explorer Pie Barchart column types (available in versions 3.5 and up).

The magnifying glass icon will apply the current configuration to the opened file in the main vlaaivis window. To reset the designer with the data that was last loaded, click the refresh icon. The help icon will get you to this page.

Configuration - General Settings (left pane)

Shows all available columns for the current dataset. Columns in bold are already present in you Pie Barchart definition.

Column Function

Name Name of the column in the dataset.
Click header to sort alphabetically (ascending / descending)

Minimum Minimum value found for this column in all rows of the current dataset.

Maximum Maximum value found for this column in all rows of the current dataset.

Type The type of the column. Click header to sort.

% Filled Graphical representation of how much rows in the dataset have non-empty values for this column.
Click header to sort (ascending / descending).

Column	Function
Name	Name of the column in the dataset. Click header to sort alphabetically (ascending / descending)
Minimum	Minimum value found for this column in all rows of the current dataset.
Maximum	Maximum value found for this column in all rows of the current dataset.
Type	The type of the column. Click header to sort.
% Filled	Graphical representation of how much rows in the dataset have non-empty values for this column. Click header to sort (ascending / descending).

Configuration - General Settings (top right pane)

General settings for the Pie Barchart.

Field Function

Name The data column that is put here will be displayed to you as identification for the rows; it's a good idea to use a column with recognizable unique values. If you are working with sets of compounds, this will typically be the JNJS id.

Preferred Ratio Defines the width of the target zone (gray outer rim) by a percentage of the pie's radius.

Field	Function
Name	The data column that is put here will be displayed to you as identification for the rows; it's a good idea to use a column with recognizable unique values. If you are working with sets of compounds, this will typically be the JNJS id.
Preferred Ratio	Defines the width of the target zone (gray outer rim) by a percentage of the pie's radius.

Configuration - Segment Configuration (bottom right pane)

Shows all columns currently represented in the Pie Barchart as well as their preferred range. Columns are grouped into segments, as can be derived from the colors.

A question mark on a red backdrop together with red a textrow indicate a validation error. Move and hold your mouse over the question mark to display a tooltip with the conflicting validation rule(s).

Click the X to remove a column from the Pie Barchart definition.

Field Function

Display Name Name shown when the user hovers the mouse pointer over this Property (wedge).

Visible Min Minimum for the value range of this Property. Values below this minimum will result in diagonally striped wedges in the Pie Barchart.

Visible Max Maximum for the value range of this Property. Values above this maximum will result in diagonally striped wedges in the Pie Barchart.

Preferred Min Lower limit of the Preferred Profile range for this property.

Preferred Value (Optional) Exact value of the outer edge of the Pie Barchart. Defaults to the average of Preferred Min and Preferred Max.

Preferred Max Upper limit of the Preferred Profile range for this property.

Converter
Algorithm used for the conversion of the data value to the percentage to fill a Property wedge by.

One of:

Normal: linear conversion based on Visible Min and Visible Max

Logarithmic: logarithmic conversion based on Visible Min and Visible Max

Lookup: conversion based on a lookup defined as in the Advanced tab. Lookup tables available by default:

Lookup(123): 0=0%, 1=10%, 2=50%, 3=100%

Lookup(YN): Y=0%, N=100%

Flip
Check to flip the range of the Property (Maximum is drawn at the pie origin, Minimum as the outer edge). Useful when lower numbers are better (and thus their wedge should be fuller) than higher numbers.

Calc Check to indicate the Property is a calculated field. All this does is adding a pattern to the wedge, as can be seen in the GREY wedges in the example Pie Barchart on top.

Weight Relative importance (as a factor) of this Property.

Description Description of the Property, shown when the user moves and holds the mouse pointer over this Property (wedge).

Designer - Advanced Tab

This tab is used to add / delete / update segments of the Pie Barchart and Lookup tables.

Segment Settings and Segment Editor

Add and Delete allow for adding and deleting segments. Use the UP and DOWN arrows to change the order of the segments. The first segment is shown at 90 degrees (3 o'clock). The rest is added clockwise.

Field	Function
Display Name	Name shown when the user hovers the mouse pointer over this Property (wedge).
Visible Min	Minimum for the value range of this Property. Values below this minimum will result in diagonally striped wedges in the Pie Barchart.
Visible Max	Maximum for the value range of this Property. Values above this maximum will result in diagonally striped wedges in the Pie Barchart.
Preferred Min	Lower limit of the Preferred Profile range for this property.
Preferred Value	(Optional) Exact value of the outer edge of the Pie Barchart. Defaults to the average of Preferred Min and Preferred Max.
Preferred Max	Upper limit of the Preferred Profile range for this property.
Converter	Algorithm used for the conversion of the data value to the percentage to fill a Property wedge by. One of: Normal: linear conversion based on Visible Min and Visible Max Logarithmic: logarithmic conversion based on Visible Min and Visible Max Lookup: conversion based on a lookup defined as in the Advanced tab. Lookup tables available by default: Lookup(123): 0=0%, 1=10%, 2=50%, 3=100% Lookup(YN): Y=0%, N=100%
Flip	Check to flip the range of the Property (Maximum is drawn at the pie origin, Minimum as the outer edge). Useful when lower numbers are better (and thus their wedge should be fuller) than higher numbers.
Calc	Check to indicate the Property is a calculated field. All this does is adding a pattern to the wedge, as can be seen in the GREY wedges in the example Pie Barchart on top.
Weight	Relative importance (as a factor) of this Property.
Description	Description of the Property, shown when the user moves and holds the mouse pointer over this Property (wedge).

Field Function

Name Name shown when the user hovers the mouse pointer over Properties of this segment (wedge).

Bar color Color of the actual wedge, representing the value of the Property.

Arc color Color of the outer edge (outline) of the segment.

Fill color Color used for the background of all the wedges in this segment.

Description Description shown when the user hovers the mouse pointer over Properties of this segment (wedge).

Field	Function
Name	Name shown when the user hovers the mouse pointer over Properties of this segment (wedge).
Bar color	Color of the actual wedge, representing the value of the Property.
Arc color	Color of the outer edge (outline) of the segment.
Fill color	Color used for the background of all the wedges in this segment.
Description	Description shown when the user hovers the mouse pointer over Properties of this segment (wedge).

Converter Settings and Lookup Converter Editor

Add and Delete allow for adding and deleting Lookup converters. Click a converter on the left to see its possible keys and matching values (as percentages, the amount of the wedge that should be filled). Use the listbox to add and delete key/value pairs