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71 Commits

Author SHA1 Message Date
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
Einar Ryeng 0df56248ee Removed obsolete module annotations. 2006-04-27 12:41:51 +00:00
Truls Alexander Tangstad fe0cf736f5 Created affy workflow. 2006-04-27 12:15:30 +00:00
Truls Alexander Tangstad 3683f6c2e9 Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot. 2006-04-27 11:38:40 +00:00
Truls Alexander Tangstad 969006015a Added LinePlot used by Affy importer. 2006-04-27 11:03:11 +00:00
Einar Ryeng 251f9d6cf4 Added command line options to create a new project based on a given workflow. 2006-04-25 12:19:25 +00:00
Einar Ryeng 359903c5ab Made system a package. 2006-04-25 09:53:35 +00:00
Arnar Flatberg cfbb76f25a import * removed 2006-04-24 16:05:54 +00:00
Einar Ryeng ba2a769f01 Function names are now folders in the navigator. 2006-04-24 15:20:27 +00:00
Einar Ryeng 179a2f88a9 The navigator now displays the plots and data in a tree that shows the ancestry information. 2006-04-24 14:52:21 +00:00
Truls Alexander Tangstad 6c72dec7fa Removed need to provide plots with project/workflow on creation, is instead injected by project itself when added to it. 2006-04-24 14:42:45 +00:00
Truls Alexander Tangstad 97e09b39a1 Added matrix-getter to Dataset. 
Added rma-function to preprocessing incorporated in AffyMatrix-importer.
Added PCAFunction to go_workflow for processing loaded affymatrix data.
 2006-04-24 14:07:34 +00:00
Arnar Flatberg cebf801cf6 bugix on creation of output data (E) from pca 2006-04-24 12:51:43 +00:00
Arnar Flatberg 6356e2ebd6 get_dim_names and get_identifiers added in dataset 2006-04-24 11:23:30 +00:00
Arnar Flatberg a2e4392a72 Complete rewrite of dataset class, with (all) the necessary updates 2006-04-24 09:53:07 +00:00
Einar Ryeng e762aef882 * system/dialogs.py: Oooops. Forgot this file in the previous commits. Well, 
here it is, currently only with the New Project dialog.
 2006-04-22 22:29:02 +00:00
Einar Ryeng f484ec9945 * workflows/go_workflow.py: Added a workflow name to make it identifiable 
in the "create project" druid.
 2006-04-22 21:48:30 +00:00
Einar Ryeng efcdafe843 * The New project toolbar button now works. A druid will display the 
available workflows and ask you to select one of them. There are still
   a couple of unresolved issues, but it works, so i upload it to ease
   the use of the program.
 2006-04-22 21:46:44 +00:00