Manipulating and editing the display
Moving the eBURST diagram:
Left clicking on a blank area of the java applet 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.
Horizontal and vertical expansion:
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.
clonal complexes can be selected and individually resized
and rotated. Selecting a subgroup founder by clicking on
it (making it green), and then shift-left clicking, allows
the whole subgroup to be moved and zoomed. You can always
return to the original diagram by clicking on ‘draw’.
You need to play with this for a while, and being under 30,
with experience of PS2 games, or a flight simulator probably
Manual editing the eBURST diagram:
eBURST v2 automatically optimises the arrangement of STs
(auto-editing) and produces eBURST diagrams that need minimal
editing. However, the manual editing features of eBURST v1
are retained 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.
To move an ST, first click on the circle representing the
ST, and a green square 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 also
Rotating and Zooming above).
Highlighting connections between
Clicking on a line between STs highlights the connecting
line in green.
The ‘Options’ button opens a new panel which
allows changes of the line thickness, font and font sizes,
colours of lines or of group and subgroup founders etc.
Removing ST labels:
In the ‘Options’ panel, the ST labels can be
removed by setting the text font size to zero.
Saving text output and eBURST diagrams:
The edited eBURST diagram, or the text output of eBURST groups
and bootstraps, can be saved to a file and then printed.
Diagrams are saved as .png graphics files and should open
in a simple photo editor (e.g. Windows Photo Editor). Text
is saved as a .txt file and will open in a text editor (e.g.
notepad). If you add no extension they will automatically
be saved as .png or .txt.
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 green. Then
clicking the ‘database’ button in the ‘Diagram
Panel’ 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 the applet from an MLST database.
Highlighting all SLVs and DLVs of a ST:
Shift and clicking on a ST shows lines from the
selected ST to all of its SLVs (pink lines) and DLVs (blue
Repeating this process removed these lines. Several STs
can be selected in turn to show the SLVs and DLVs of multiple
STs. Shift and clicking on a link (line) between two STs
shows the SLVs and DLVs of both of the linked 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. If you
are having difficulties selecting what you want, you can
first click on the ST, line, clonal complex, to activate
it (make it green), and then press shift and click on it
again. These are all toggles and so repeating the process
removes the lines. Hint – you can always remove all
the lines if you press ‘draw’ to refresh the
Re-assigning the primary founder:
the ST you wish to assign as the primary founder and then
click ‘Founder’ in the ‘Diagram Panel’.
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’.