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condition tree authored by Thomas Van Parys's avatar Thomas Van Parys
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......@@ -7,7 +7,7 @@ Creation of images relies on at least two types of data: the data matrix and the
* **data matrix**: The expression data. The header contains the name of all experiments (conditions), the first column represents gene names. The rest of the data consists of the expression data.
* **gene file**: Either an [XML file](TreeFile) with modules and genes, possibly grouped together into a tree structure, or a [simple list](ListFile) of modules with their genes.
* **condition tree**: (optional) [XML file](TreeFile) with conditions to be displayed per module, possibly grouped together into a tree structure.
* **condition tree**: (optional) By default, each module displays all conditions, in the same order as given in the expression matrix. A more fine grained representation can be defined using an [XML file](TreeFile). This file specifies conditions to be displayed per module, possibly grouped together into a tree structure.
* **regulator tree**: (optional) [XML file](TreeFile) with regulator genes or a [simple list](ListFile) of regulators assigned to modules.
* **symbolic name mapping**: A tab delimted two column mapping file: GeneID --> Symbolic Name
* **annotations**: Most information that should be drawn around the central module matrices, can be described as: "Module number x lists genes or conditions y1, y2, y3, ... as having property z". Optionally each gene or condition can be linked to an extra data point (color, integer, ...). For this purpose, we created the [MVFFormat](MVFFormat).
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