ae9a207a71
Added a tag column in the GO browser to help link it to selections.
2007-03-01 19:13:13 +00:00
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
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
f612dda72f
Fixed bug in ftsv save and open dialogs. The save dialog now looks as intended.
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Added the possibility to load several datasets at once. Error handling should still
be improved.
2007-01-16 12:28:56 +00:00
58886726d8
Small updates.
2007-01-12 10:50:55 +00:00
ae3aa7e4aa
Create Resnik distances and save them as ftsv.
2007-01-12 00:00:56 +00:00
e4d7f8e5a2
Resnik distances between GO terms work now.
2007-01-11 22:01:31 +00:00
4b1d16ea78
Updated go-workflow.
2007-01-11 18:57:45 +00:00
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
060732d980
More persumably non-working stuff.
2007-01-10 15:33:19 +00:00
1e0b99f283
small bugfix
2007-01-09 08:53:28 +00:00
fa047e0171
Committing non-working code that breaks go workflow. ;)
2007-01-08 21:13:22 +00:00
fac9346aad
Added very hackish annotation count reader.
2006-12-15 12:53:27 +00:00
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
0b30aeac6f
Updated GO workflow.
2006-10-22 23:19:54 +00:00
5491f5ce04
GO workflow. Does not work.
2006-10-22 15:31:36 +00:00
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
86f89b6ffe
Typo.
2006-05-09 13:51:14 +00:00
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
0db25f1dd7
Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it.
2006-05-05 14:43:53 +00:00
56a6028547
Validation on number of inputs added
2006-05-03 11:52:54 +00:00
5b2223afcd
Multiselection included. (Without input validation).
2006-05-03 11:11:45 +00:00
0df56248ee
Removed obsolete module annotations.
2006-04-27 12:41:51 +00:00
3683f6c2e9
Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot.
2006-04-27 11:38:40 +00:00
969006015a
Added LinePlot used by Affy importer.
2006-04-27 11:03:11 +00:00
251f9d6cf4
Added command line options to create a new project based on a given workflow.
2006-04-25 12:19:25 +00:00
359903c5ab
Made system a package.
2006-04-25 09:53:35 +00:00
ba2a769f01
Function names are now folders in the navigator.
2006-04-24 15:20:27 +00:00
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
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
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
a2e4392a72
Complete rewrite of dataset class, with (all) the necessary updates
2006-04-24 09:53:07 +00:00
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
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
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
26f16acc9c
Made sure pickling use protocol 2 to make it faster and the files smaller (binary).
2006-04-22 18:11:31 +00:00
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
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
d123f0e1c1
Added doc-string for CelFileImportFunction.
2006-04-22 15:59:19 +00:00
23914b2d1e
Added support for affy cel files.
2006-04-22 00:17:22 +00:00
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
efcd8c8587
Removed unused code.
2006-04-21 15:00:04 +00:00
79481ed186
Added plot to output from test-function.
2006-04-21 14:58:42 +00:00
07ac564668
Changed info function to show dialog instead of returning a view.
2006-04-21 14:12:18 +00:00
c4f9f5c399
Created new workflow for showing information about a dataset as a view.
2006-04-21 13:04:31 +00:00
ccec17262b
Added random test data
2006-04-21 10:56:01 +00:00
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
6a4ae8ecf1
mainly overhaul of observers, and removal of project singleton
2006-04-20 10:27:58 +00:00
f45c9c6bf7
* fluent: General cleanup.
2006-04-19 19:59:55 +00:00
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
