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## ModuleViewer Format #########
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*Annotations*, either for genes or for conditions, are grouped into *blocks*. Each block consist of a certain type of annotation that will be drawn together. An Annotation is one line that can be interpreted as "This module has a list of items that are annotated with this property".
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The header of a block starts each line with `::` and consists of `key=value` pairs.
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Possible keys:
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* **TYPE**: this tells the viewer how to treat this block. The type will also be used as a default label for the block.
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By default, annotation blocks are drawn as colored matrices, so TYPE can be any value describing the type of data represented here (go, TF enrichment, core, etc, ...).
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A few types are reserved words, which will be represented differently:
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Blocks that highlight genes or regulators names:
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* genecolorbox
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* regulatorcolorbox
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Blocks that are drawn as edges on the left side of the figure:
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* regulator-regulator interaction
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* regulator-gene interaction
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* gene-gene interaction
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* **TITLE**: Optional label for the block.
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* **OBJECT**: Either `GENES` or `CONDITIONS`, depending on what you're annotating. `GENE` blocks will be drawn right of the expression matrix. `CONDITIONS` blocks are drawn below it.
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* **COLOR**: The color to use when drawing.
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* **VALUES**: Either `None` (or just omit the `VALUES` line), `COLOR` or `NUMBER`, depending on what extra information is linked to the individual genes.
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* **GLOBAL**: Allows you to drop the first column (module id). Annotations will be drawn the same for every module.
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* **VALUE_SEPARATOR**: Changes the default key-value separator ':' to something else. Useful when items names contain ':' themselves.
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* **LEGEND**: Construct a Legend block below the figure. The value of this key is constructed like any annotation line (see example)
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Format:
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`ModuleId TAB Gene list (pipe delimited) TAB Annotation name (optional)`
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The genes in the gene list can be linked to a value (color or number, as set in the VALUES header) as `Gene:value` pairs.
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Example:
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```
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::TYPE=reg_rank
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::TITLE=Regulator ranking
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::VALUES=color
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::OBJECT=REGULATORS
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101 AT3G22780:#CCCCFF|AT4G00130:#DADAFF ranking
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101 AT3G22780:#FF0000|AT4G00130:#FFEAEA percentage
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```
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This small block will draw an annotation block next to the regulators of module 101. It will have as many rows as there are regulators and will have two columns: ranking and percentage.
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In the ranking column, the regulators `AT3G22780` and `AT4G00130` will be marked with a shade of blue. In the percentage column, `AT3G22780` and `AT4G00130` are marked with shades of red.
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Color codes can be defined by name, RGB code or Java color int.
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Example:
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```
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::VALUE_SEPARATOR=//
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::LEGEND=SA+//MAGENTA|ABA+//RED|MJ+//YELLOW|BR-//CYAN|BR+//ORANGE|ET+//GRAY|AUXIN-//GREEN|AUXIN+//BLUE|ET-//BLACK hormones
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```
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This will add a legend to this block with the label 'hormones'. Hormones SA+, ABA+, BR-, etc... are respectively shown with the colors magenta, red, yellow, ... |
