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88 Commits

Author SHA1 Message Date
Einar Ryeng d6298a2d99 Ensures that the GO is only loaded once. 2007-06-21 10:26:35 +00:00
Arnar Flatberg dbe49b366d added import of networkx 2007-03-15 10:38:05 +00:00
Einar Ryeng f6696dfacc Added gobrowser to smalltest workflow. 2007-03-14 21:08:56 +00:00
Arnar Flatberg 6cbf6d0689 Initial commit of small example test workflow 2007-03-13 15:24:20 +00:00
Einar Ryeng ae9a207a71 Added a tag column in the GO browser to help link it to selections. 2007-03-01 19:13:13 +00:00
Einar Ryeng 89636962a7 Added Workflow.get_data_file_name() which returns the full path to a given 
data file, or None if the file does not exist. This is tested in the test
workflow.
 2007-02-28 14:56:24 +00:00
Arnar Flatberg a7c60ffe64 added venn diagram test plot 2007-01-31 13:03:27 +00:00
Einar Ryeng a65d79697f Added Expand/Collapse menu choices to the GO browser context menu. This is 
particularly useful when searching for GO terms, because the gtk TreeView
widget does not do interactive search in collapsed parts of the tree.
 2007-01-21 16:16:37 +00:00
Einar Ryeng 7693f336ba Added a singleton project in the project module, so that the current project is 
easily accessible from anywhere in the code. As there is only one project at
any given time this should not be a problem.

The Gene Ontology browser needed this to be able to set the selection without
passing the current project through several constructors. 

Added a context menu in the GO browser that allows the user to select all GO
terms in the subgraph that starts on the current node.
 2007-01-18 15:45:48 +00:00
Einar Ryeng c3c6e85044 Added ImagePlot, which displays a dataset as an image. 2007-01-17 13:20:04 +00:00
Einar Ryeng f612dda72f Fixed bug in ftsv save and open dialogs. The save dialog now looks as intended. 
Added the possibility to load several datasets at once. Error handling should still
be improved.
 2007-01-16 12:28:56 +00:00
Einar Ryeng 58886726d8 Small updates. 2007-01-12 10:50:55 +00:00
Einar Ryeng ae3aa7e4aa Create Resnik distances and save them as ftsv. 2007-01-12 00:00:56 +00:00
Einar Ryeng e4d7f8e5a2 Resnik distances between GO terms work now. 2007-01-11 22:01:31 +00:00
Einar Ryeng 4b1d16ea78 Updated go-workflow. 2007-01-11 18:57:45 +00:00
Einar Ryeng 9274b044b7 Added read_ftsv in dataset.py. This method reads fluents tab separated values 
files and returns a dataset.
 2007-01-10 17:35:58 +00:00
Einar Ryeng 060732d980 More persumably non-working stuff. 2007-01-10 15:33:19 +00:00
Arnar Flatberg 1e0b99f283 small bugfix 2007-01-09 08:53:28 +00:00
Einar Ryeng fa047e0171 Committing non-working code that breaks go workflow. ;) 2007-01-08 21:13:22 +00:00
Einar Ryeng fac9346aad Added very hackish annotation count reader. 2006-12-15 12:53:27 +00:00
Einar Ryeng fb77ddb549 Updated GO workflow. Options class test added. Reading the ontology takes too 
long.
 2006-10-26 16:51:42 +00:00
Einar Ryeng 0b30aeac6f Updated GO workflow. 2006-10-22 23:19:54 +00:00
Einar Ryeng 5491f5ce04 GO workflow. Does not work. 2006-10-22 15:31:36 +00:00
Einar Ryeng 375d45e0cc Updated import statements, and removed the workflows pca_workflow and 
affy_workflow.
 2006-10-17 14:42:27 +00:00
Arnar Flatberg c40f9a2947 Added a LineViewPlot in GenerateData 2006-10-17 13:59:31 +00:00
Einar Ryeng e0ca48d4b3 Changed how the selection list works. CategoryDatasets can be dragged down to 
the selection list, and will then be converted to Selections.
 2006-09-08 18:25:03 +00:00
Einar Ryeng f47a9066e3 Removed print statements. 2006-08-31 12:24:06 +00:00
Arnar Flatberg 0b58c5ea28 Switch to numpy (scipy_version>1.0) changes 2006-08-31 10:04:19 +00:00
Einar Ryeng a0786d521a Removed SinePlot from the test workflow. 2006-08-30 14:38:33 +00:00
Einar Ryeng 1b9aff1c5a The selection view now works. Functions can return a dataset.Selection object which will be stored in the selection list. 2006-08-29 23:57:21 +00:00
Arnar Flatberg 97e652edce fixes 2006-08-28 12:06:05 +00:00
Arnar Flatberg fc8b2e601f update 2006-08-14 11:52:26 +00:00
Einar Ryeng b769288b3b Added a selection view tab, placed next to the "Log" tab. The tab currently 
only displays the current selection.
 2006-08-07 14:14:42 +00:00
Einar Ryeng 4c716e9428 NetworkPlot now works, but does not allow node colors or sizes to be passed as keyword arguments. 2006-08-03 14:30:06 +00:00
Einar Ryeng b3d681ef16 * system/plots.py: Added NetworkPlot, which may or may not work correctly. 
* system/dataset.py: Removed a few lines of obsolete code.
 2006-08-01 13:22:39 +00:00
Einar Ryeng 87f87e36c8 * system/fluents.py: Fixed a bug where the the application tried to load 
a toolbar from None

 * system/plots.py: Fixed MainView.insert_view that was a no-op when in large
   view.

 * system/dataset.py: Changed __str__ of dataset to also show names of dimensions.
 2006-07-21 14:30:09 +00:00
Truls Alexander Tangstad 9ab1ebe687 Small cleanup. 2006-05-09 14:16:22 +00:00
Truls Alexander Tangstad 443b18cea6 Made sure ordering of matrices are ok. 2006-05-09 14:13:09 +00:00
Truls Alexander Tangstad 86f89b6ffe Typo. 2006-05-09 13:51:14 +00:00
Truls Alexander Tangstad 5b1af849dc Implemented Limma function for Affy workflow. 
Extended ScatterPlot to take two datasets and updated code using it.
 2006-05-09 13:17:17 +00:00
Truls Alexander Tangstad 0db25f1dd7 Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it. 2006-05-05 14:43:53 +00:00
Truls Alexander Tangstad 97f56f66ac Added text-input for contrast-matrix creator for affymetrics workflow. 2006-05-05 14:30:23 +00:00
Truls Alexander Tangstad aa3a9ab619 Added automagic argument checking when running functions. 2006-05-05 10:10:03 +00:00
Truls Alexander Tangstad fafa373e67 Added categorygetter for PhenotypeDataset. 2006-05-04 13:30:04 +00:00
Truls Alexander Tangstad fb7128138e Fixed floats in phenotype importer. 
Added PrintFunction for debug-printing.
Added PhenotypeImportFunction to AffyWorkflow.
 2006-05-03 14:27:38 +00:00
Truls Alexander Tangstad b757da5929 Implemented PhenotypeDataset with tests. 2006-05-03 14:04:28 +00:00
Reidar Strand Hagen 56a6028547 Validation on number of inputs added 2006-05-03 11:52:54 +00:00
Reidar Strand Hagen 5b2223afcd Multiselection included. (Without input validation). 2006-05-03 11:11:45 +00:00
Truls Alexander Tangstad a2d3a9d5cc Made PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input. 2006-04-28 11:44:55 +00:00
Truls Alexander Tangstad 8fd1f4ba83 Renamed module for affy workflow. 2006-04-27 15:06:01 +00:00