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
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
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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
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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
87f87e36c8
* system/fluents.py: Fixed a bug where the the application tried to load
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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
86f89b6ffe
Typo.
2006-05-09 13:51:14 +00:00
Truls Alexander Tangstad
5b1af849dc
Implemented Limma function for Affy workflow.
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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
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
Einar Ryeng
0df56248ee
Removed obsolete module annotations.
2006-04-27 12:41:51 +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
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.
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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
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,
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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
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in the "create project" druid.
2006-04-22 21:48:30 +00:00
Truls Alexander Tangstad
357cd1a1a6
Removed workflow being dependent on rpy by putting the import within the run function of affymatrix import.
2006-04-22 20:48:44 +00:00
Truls Alexander Tangstad
26f16acc9c
Made sure pickling use protocol 2 to make it faster and the files smaller (binary).
2006-04-22 18:11:31 +00:00
Truls Alexander Tangstad
553bfbe1ae
Big cleanup of affymatrix importer. Now use E@exprs to get matrix from loaded data.
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Also made row and colname import better by ensuring vector-handling, ensuring that getting single column/row data works without being converted into a single string instead of string in a list.
Removed ;1-hack and use NO_CONVERSION to ensure no extra computation is done when calculating r stuff.
Now AffyMatrix data is named as such.
2006-04-22 17:59:15 +00:00
Truls Alexander Tangstad
5a2a1afe91
Added pickling as a quick and dirty way of loading and saving data in einars workflow.
2006-04-22 16:27:33 +00:00
Truls Alexander Tangstad
d123f0e1c1
Added doc-string for CelFileImportFunction.
2006-04-22 15:59:19 +00:00
Truls Alexander Tangstad
23914b2d1e
Added support for affy cel files.
2006-04-22 00:17:22 +00:00
Truls Alexander Tangstad
c601ad3966
Removed data information as function in workflow and added as default action on datasets double-clicked in navigator.
2006-04-21 15:02:13 +00:00
Truls Alexander Tangstad
efcd8c8587
Removed unused code.
2006-04-21 15:00:04 +00:00
Truls Alexander Tangstad
79481ed186
Added plot to output from test-function.
2006-04-21 14:58:42 +00:00
Truls Alexander Tangstad
07ac564668
Changed info function to show dialog instead of returning a view.
2006-04-21 14:12:18 +00:00
Truls Alexander Tangstad
c4f9f5c399
Created new workflow for showing information about a dataset as a view.
2006-04-21 13:04:31 +00:00
Arnar Flatberg
ccec17262b
Added random test data
2006-04-21 10:56:01 +00:00
Einar Ryeng
c09f2ceb92
* fluent, *.py: Data and plots returned from functions will now show up in
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the navigator window.
2006-04-20 14:29:13 +00:00
Arnar Flatberg
6a4ae8ecf1
mainly overhaul of observers, and removal of project singleton
2006-04-20 10:27:58 +00:00
Einar Ryeng
f45c9c6bf7
* fluent: General cleanup.
2006-04-19 19:59:55 +00:00
Einar Ryeng
c55a39f7f9
* workflows/go_workflow.py: A workflow that makes distance matrices based
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on gene ontology information. Currently only reads gene annotations.
2006-04-17 20:29:29 +00:00
Einar Ryeng
Arnar Flatberg
Truls Alexander Tangstad
Reidar Strand Hagen