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Customizing ArrayMiner's graphics
- Select the colors used in Heat Maps: you can select
the colors representing the low/flat/high expression levels in heat
maps. For instance, instead of the classic green/black/red palette,
you may opt for the more pleasing blue/yellow/red one.
- Select the colors of your clusters in 2D&3D: should the
default colors used by ArrayMiner to draw the 2D&3D points and convex
hulls not satisfy you, you may change
the palette
- Name your clusters and show the labels in 2D&3D: some or
all of your clusters may suggest meaningful names, such as "Ascending",
"Periodic", etc. You can assign
such names to your clusters - the names are then displayed, instead
of the default cluster IDs, in the 2D
and 3D views
- Color individual profiles with Coloring Schemes: you can create
coloring schemes
that distinguish individual profiles. For instance, you may have a list
of genes you would like to highlight in ArrayMiner's graphics, or would
like to show how an external classification (e.g. an ontology) matches
your clusters - all you need is to create a coloring
scheme. You can also directly read GeneSpring classifications to
be used as coloring schemes
- Use the Heat Map Publisher: the Publisher
gives you an extensive set of controls to create a presentation of your
results compatible with most journal formats
Exporting graphics
- Save high-resolution graphics into files: there is no need
to limit yourself to the necessarily low resolution of the computer
screen - most of ArrayMiner's graphics can be exported
into graphic files at resolutions of your choosing
- Paste high-resolution graphics directly into your document
(PC only): you can paste ArrayMiner's
graphics into your document or presentation directly, without the need
of intermediate graphic files. Selecting the 96dpi units will even tell
you in advance the size of the image when printed
Publishing on the Web
- Create interactive (movable) applets from your 3D views: there
is no more intuitive way of representing the relationships among your
expression profiles than ArrayMiner's 3D
view. As of version 5.1, with a few mouse clicks, you can create
interactive Java applets viewable in a simple Web browser, where
it can be rotated, zoomed, etc., much as in ArrayMiner itself. The applets
can be then made available on the Web as supplementary material for
publications, or used during live presentations. Have a look at a running
example on the Web.
- Create pleasing tabular presentation of your clusters: just
two mouse clicks are necessary to generate a complete and pleasing report
in HTML that can be made available on the Web. The HTML files generated
by ArrayMiner are also directly readable by popular spreadsheet programs
such as Microsoft Excel, where they can be reedited if necessary.
Describing your clustering work
- Get the sentence that describes the clustering process: the
sentence contains all the information necessary for a publication, and
is copied into the clipboard
with a single mouse click, ready to be pasted into your document.
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