Einar Ryeng
884804c49a
Added a dummy for the t-test function. Will be updated when I have access to my
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office computer tomorrow.
2007-06-28 21:48:13 +00:00
Einar Ryeng
7b20f44fef
Added a GO similarity function that does not do anything useful yet.
2007-06-22 15:37:59 +00:00
Einar Ryeng
e5cd8a8077
Started on a function to enhance gene lists by using GO similarities.
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Not in a usable state.
2007-06-22 15:37:22 +00:00
Einar Ryeng
ff8833a22c
Added read functions for the medium and large smokers sets.
2007-06-21 10:28:10 +00:00
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
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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
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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
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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.
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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
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
375d45e0cc
Updated import statements, and removed the workflows pca_workflow and
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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
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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
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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.
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* 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
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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
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.
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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
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.
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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
Einar Ryeng
Arnar Flatberg
Truls Alexander Tangstad