and editing the eBURST diagram.
Moving the eBURST
Left clicking on a blank area of the diagram window and moving the mouse allows
the diagram to be dragged around the screen. Where there are multiple unlinked
clusters, clicking within an individual cluster produces a green rectangle
around it and the mouse can be used to drag that individual cluster around
the screen. If you have difficulty selecting a clonal complex, you can click
on any line between two of the STs in the complex (the line goes green), and
then left clicking allows the whole complex to be moved. Clicking on a line
also allows pairs or triplets (etc) of STs to be moved together. Clicking in
an area outside (or between) the clusters allows you to return to the default
where the mouse drags the whole diagram around the screen.
Holding down the ‘Alt’ key, left clicking and moving the mouse
allows the diagram to be expanded or contracted in the up-down and left-right
dimensions. This can also be used to change the shape of individual selected
clonal complexes in diagrams that contain multiple complexes. This is useful
as sometimes autoediting produced elliptical diagrams which can be made circular
using this editing feature.
Rotating and zooming:
Holding down the shift key, left clicking and
moving the mouse allows the diagram to be re-sized and
rotated. Individual clonal complexes can be selected and
individually resized and rotated. Selecting a subgroup
founder by clicking on it (making it red), and then shift-left
clicking, allows the whole subgroup to be moved and zoomed.
You can always return to the original diagram by clicking
You need to play with this for a while, and being under 30, with experience
of PS2 games, or a flight simulator probably helps.
the eBURST diagram:
eBURSTv3 automatically optimises the arrangement of STs (auto-editing) and
produces eBURST diagrams that need minimal editing. Manual editing features
can also be used and where necessary, can convert the initial auto-edited eBURST
diagram into an optimal eBURST diagram for use in a publication or a Powerpoint
presentation. A new feature of eBURSTv3 is the ability to save a diagram in
SVG format. This allows further changes to the diagrams to be undertaken using
third party SVG editors.
To move an ST, first click on the circle representing the ST, and a red halo
appears around the circle to show it has been selected (you may have to move
the mouse around slightly to find exacting the right place to click). The selected
ST can then be dragged to the required position by moving the mouse. Where
there are linked STs that need to be re-positioned, dragging an external ST
will move only that ST, whereas dragging an internal ST will move the whole
group of linked STs. This prevents the linkages between STs being inadvertently
altered while editing the diagram. All of the STs in a subgroup can now be
moved together (see section 9.3).
connections between STs:
Clicking on a line between STs highlights the connecting line in green.
Text size and
font of ST labels:
In the ‘Diagrams’ menu the
Colour Options opens the Properties
Panel and the text style (font and
font size etc) of ST labels can be changed
A key displaying the default colour coding for elements of the diagram can
be viewed to aid interpretation. Should any changes to the default colours
be made these will not however be reflected in the key.
Changing default colours and
You can change all colours from their defaults through the ‘colour options’ section
of the diagram menu.
Show ST labels:
By default, this option is checked, unchecking removes all text from an eBURST
diagram. Should you be comparing two datasets coloured ‘halos’ will
appear surrounding STs to show in which dataset they are represented.
Saving text output:
The textual output of eBURST groups and bootstraps
can be saved to a file through the ’Save’ option
of the File menu, when the Analysis TAB is selected
eBURST diagrams can be saved in the following formats –
Of particular use is the ability to save
in the Scaleable Vector Graphic (SVG)
format. SVG is an XML representation of
vector images and as such allows the eBURST
diagram to be re-edited using 3rd party
To view SVG documents you need an SVG
viewer which comes in the form of a plug-in
for web browsers. The plug-in is freely
available and can be downloaded from http://www.adobe.com/svg/
To further edit eBURST diagrams saved
in SVG format we recommend using either
the commercial software Adobe Illustrator
(www.adobe.com), or freeware editors such
as the W3C recommended Amaye – (www.w3.org/Amaya/)
or Inkscape (www.inkscape.org).
Printing eBURST diagrams and
eBURST diagrams can be printed through
the File menu ‘print’ option.
Obtaining more information about
groups or STs:
Further information can be obtained about
the STs from within an eBURST diagram.
The ST of interest should be selected
by clicking on it until it becomes red.
Then selecting the ‘database’ option
in the ‘Diagram menu’ will
open a new panel with the selected ST
number already entered. Isolates of the
selected ST within the MLST database are
returned as the default. Ticking the ‘+
SLVs’ box returns details of the
selected ST and all of its SLVs. Obviously
linking from the eBURST diagram to a MLST
database only works for data submitted
to eBURST from an MLST database
Highlighting all SLVs and DLVs of a ST:
You can view all SLV links or all DLV
links of a particular ST or entire clonal
complex by using the checkboxes located
in the Diagram Panel. After checking either
SLV, DLV or both, select an ST by clicking
it (a red halo appears around the ST)
The diagram now displays lines from the
selected ST to all of its SLVs (pink lines)
and/or DLVs (blue lines). You can remove
the lines by unchecking the boxes. Several
STs can be selected in turn to show the
SLVs and DLVs of multiple STs. Shift and
clicking within a clonal complex shows
all of the SLVs and DLVs of all of the
STs within the clonal complexes. Shift
and clicking on an empty area of the diagram
shows all of the SLV and DLV links of
all of the STs.
Hint – you can always remove all
the lines if you press ‘draw’ to
refresh the diagram.
Re-assigning the primary founder:
From the Diagram TAB, click/highlight
the ST you wish to assign as the primary
founder and then click ‘Founder’ in
the ‘Diagram menu’. The new
auto-edited eBURST diagram is drawn, with
the user-defined primary founder’ in
red, to show that you, rather than eBURST,
have made this assignment of the primary
founder. Note that the number of SLVs
linked to the selected primary founder
may well increase considerably (compared
to the original eBURST diagram) as all
its SLVs will now be preferentially assigned
to the new ‘founder’.