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## About ###
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The ModuleViewer project was originally started to browse [[LeMoNe]] and [[Enigma]] output efficiently on a desktop pc and independently of the rest of both applications that generate the data. We also wanted one common viewer to maintain, that could handle both data generated by Enigma and LeMoNe.
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Both applications were slightly altered to generate compatible output.
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By separating the graphical libraries and the GUI application with parsers, and by keeping the code as generic as possible, ModuleViewer became a handy tool to generate figures for all kinds of expression matrices and their associated data.
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Click [here][presentation] to download a short presentation about ModuleViewer (BEG Lunch Meeting of 25 Oct. 2011.
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[presentation]: <wiki/docs/moduleviewer.odp>
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## File Type ####
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Creation of images relies on at least two types of data: the data matrix and the modules file. Optionally, this can be extended with regulator data, a condition tree, and annotation files.
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* **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.
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* **gene file**: Either an XML file with modules and genes, possibly grouped together into a tree structure, or a simple list of modules with their genes.
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* **condition tree**: (optional) XML file with conditions to be displayed per module, possibly grouped together into a tree structure.
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* **regulator tree**: (optional) XML file with regulator genes or a simple list of regulators assigned to modules.
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* **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]].
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Demo data can be downloaded here: [[ModuleViewerDemoData]].
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## Running ModuleViewer ######
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### Start ModuleViewer ####
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[](http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp)
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### Pre-loaded data ####
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[](http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp?expmatrix=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered&modules=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_geneTree.xml&conditions=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_conditionTree.xml®ulators=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_regulatorTree.xml&annotations=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/Annotations.mvf)
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### Run locally ###
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Alternatively, you can clone the code from the repository (master or stable tag), compile it using [maven][] and run it from the command line. Maven will take care of downloading the dependencies. The dependency on [ModuleGraphics][] is not served from any maven repository (yet), so you first need to clone that code and also maven install it as well.
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A GUI will be launched from which you can load your data and browse the output figures.
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[webstart]: http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp
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[maven]: https://maven.apache.org/
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[ModuleGraphics]: https://gitlab.psb.ugent.be/thpar/ModuleGraphics
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## Command line options #########
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Both the command line and the webstart version allow to specify input files at launch. This allows an application or pipeline to automatically open ModuleViewer to show output figures.
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Files can be either local files or URLs.
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```
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usage: ModuleViewer
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-a,--annotations <annotation file> One or more MVF annotation files
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-c,--conditions <condition file> Condition tree file
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-e,--expmatrix <matrix file> The expression matrix
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-h,--help Show this help
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-m,--modules <module file> Module file (XML or flat list)
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-r,--regulators <regulator file> Regulator file (XML or flat list)
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-s,--synonyms <synonym file> Gene ID - synonym mapping
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```
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Launch the viewer with demo data [pre-loaded][].
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[pre-loaded]: http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp?expmatrix=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered&modules=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_geneTree.xml&conditions=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_conditionTree.xml®ulators=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/hughratcur_nan_filtered_regulatorTree.xml&annotations=http://bioinformatics.psb.ugent.be/webtools/moduleviewer/testdata/Annotations.mvf
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