| ... | ... | @@ -6,10 +6,10 @@ ModuleViewer is a tool to directly generate annotated heat maps from gene cluste |
|
|
|
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.
|
|
|
|
|
|
|
|
* **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 with modules and genes, possibly grouped together into a tree structure, or a simple list of modules with their genes.
|
|
|
|
* **condition tree**: (optional) XML file with conditions to be displayed per module, possibly grouped together into a tree structure.
|
|
|
|
* **regulator tree**: (optional) XML file with regulator genes or a simple list of regulators assigned to modules.
|
|
|
|
* **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]().
|
|
|
|
* **gene file**: Either an [XML file](TreeFile) with modules and genes, possibly grouped together into a tree structure, or a simple list 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.
|
|
|
|
* **regulator tree**: (optional) [XML file](TreeFile) with regulator genes or a simple list of regulators assigned to modules.
|
|
|
|
* **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).
|
|
|
|
|
|
|
|
Demo data can be downloaded here: [ModuleViewerDemoData](ModuleViewerDemoData).
|
|
|
|
|
| ... | ... | @@ -20,15 +20,13 @@ Demo data can be downloaded here: [ModuleViewerDemoData](ModuleViewerDemoData). |
|
|
|
|
|
|
|
[](http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp)
|
|
|
|
|
|
|
|
### Pre-loaded data ####
|
|
|
|
### Demo with pre-loaded data ####
|
|
|
|
|
|
|
|
[](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)
|
|
|
|
|
|
|
|
### Run locally ###
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
A GUI will be launched from which you can load your data and browse the output figures.
|
|
|
|
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 need to clone that code and maven install it first.
|
|
|
|
|
|
|
|
[webstart]: http://bioinformatics.psb.ugent.be/webtools/moduleviewer/launch.jnlp
|
|
|
|
[maven]: https://maven.apache.org/
|
| ... | ... | @@ -48,9 +46,4 @@ usage: ModuleViewer |
|
|
|
-m,--modules <module file> Module file (XML or flat list)
|
|
|
|
-r,--regulators <regulator file> Regulator file (XML or flat list)
|
|
|
|
-s,--synonyms <synonym file> Gene ID - synonym mapping
|
|
|
|
```
|
|
|
|
|
|
|
|
Launch the viewer with demo data [pre-loaded][].
|
|
|
|
|
|
|
|
[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
|
|
|
|
|
|
|
|
``` |
|
|
\ No newline at end of file |
