Plant Bioinformatics Group

Manual

Instructions for use

Topics:
Data format
Loading data
Choosing data to display
View controls
Background colour
Highlighting subsets of data
Exploring individual data points

Data format

Legacy data format

The minimum requirement for data is that there are at least three data variables available for display. Data must be in supplied by the user in a tab-delimited text file, with the column order as follows:

Category data --> Labels for individual data points --> Data column 1 --> Data column 2 --> ..... Data column n

If your data does not have category information attached to it, the entire first column can be left empty.

There is no limit on the number of data columns but the data in these must obviously be numerical. Columns can be labelled with any label. Make sure there are no extra lines or tabs after the end of the data in either direction.

New multi-category data format

This format is supported from version 1.10.12.10 onwards and supports multiple columns with category information, allowing users to categorize their data in different ways. The legacy format is still supported.

The basic format is as described above, but category column headers must starts with the prefix "categories:" and there can be an unlimited number of these to the left of the column with the data labels:

Category data1 --> category data2 --> .... category data n --> Labels for individual data points --> Data column 1 --> Data column 2 --> ..... Data column n

Thus, the data headers might look something like this:

categories:size --> categories:age --> myLabels --> PCO1 --> PCO2 --> PCO3

An example file with multi-category data is available.

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Loading data

Go to File --> Open... and select a file of choice. If you would like to experiment with some example data, go to File --> Load example data. This will load a file supplied with the application which contains randomly generated data. You can use this to explore the functionality of the application.
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Choosing data to display

On the left hand control panel, select for each axis from the drop-down menu which variable you would like displayed.
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View controls

To reorient the graph, click and drag with the left mouse button. To go back to the original viewpoint, click the button labelled "Reset Viewpoint".

To zoom in and out, middle-click and drag or Alt+Left-click and drag.
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Background colour

Select this from the drop-down menu at the top of the left hand control panel. Options are light grey, dark grey, black and white.
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Highlighting subsets of data

You can selectively colour data from one or more categories by clicking on them in the category list panel on the bottom left (Ctrl + click to select more than one category). This will grey out all data points except for those in the selected categories.

To show the original colouring again, press the button labelled "Reset Selection".
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Exploring individual data points

Position the mouse over a data point and its individual label (as supplied in the data file) will be displayed in the status bar at the bottom left corner of the application.

Users can also enter an annotation URL for data points (File -> Annotation URL...) and this then allows them to click on a data point which results in the default web browser being started up with a URL constructed by the application. The annotation URL entered by the user needs to be such that the name (label) of the data point can be appended to it to form a valid URL, for example:


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