Einar Ryeng
7e6bac20e1
FIXING STUFF!
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Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
Arnar Flatberg
b313cf29bc
Workflow updates
2008-02-29 16:23:57 +00:00
Arnar Flatberg
e417547923
cc
2008-02-06 09:42:46 +00:00
Arnar Flatberg
14d24d02c2
Demo workflow
2008-02-05 11:34:14 +00:00
Einar Ryeng
ca267920d8
Removed a couple of output datasets that did not work from pls.
2008-01-07 10:47:17 +00:00
Einar Ryeng
4de9a58ae9
Made a LoadDataFunction instead of four almost identical specialiced Funcions.
2007-12-14 16:45:05 +00:00
Einar Ryeng
a94c3ed1cc
Smoker workflow now loads data from correct path.
2007-12-14 15:15:01 +00:00
Arnar Flatberg
aef2e1daf0
Tralala ...
2007-11-07 12:34:13 +00:00
Arnar Flatberg
ffe1ce6319
Fixed queries
2007-08-22 13:40:33 +00:00
Arnar Flatberg
d510e092e3
Added SAM and conditioned enrichment analysis
2007-08-14 16:16:31 +00:00
Einar Ryeng
13b35180ee
Fixed bug in DAG plot color mapping.
2007-08-08 12:24:14 +00:00
Einar Ryeng
4b80baf225
Added information content drag'n'drop to z loadings plot.
2007-08-06 16:20:39 +00:00
Einar Ryeng
3f7215bc35
Factored out a mixin class for IC thresholding.
2007-08-03 12:09:17 +00:00
Einar Ryeng
94f4b276b9
Fixed selection in DAG-plot to work both with and without IC set.
2007-08-02 11:20:30 +00:00
Arnar Flatberg
2d419a9862
Added GO-category enrichment analysis
2007-08-02 11:18:48 +00:00
Einar Ryeng
b233e4abc6
Added spin buttons for minimum and maximum information content in DAG plot.
2007-08-02 10:20:33 +00:00
Einar Ryeng
aa4007e208
Improved drag'n'drop of data into scatter plots so that it no longer requires
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matching identifiers along dimensions.
2007-07-30 17:42:48 +00:00
Einar Ryeng
0bc4a6e3f0
Fixed drag'n'drop of datasets to DAG-plots to convert inf/-inf to
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maximum/minimum values of the dataset.
2007-07-30 14:15:23 +00:00
Einar Ryeng
e84a202fbe
Commented out unused functions.
2007-07-30 10:51:58 +00:00
Einar Ryeng
dc7f7dbde2
Added existing_identifiers function to Dataset.
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Added colouring drag'n'drop to DAGPlot in gobrowser module.
2007-07-26 15:45:42 +00:00
Einar Ryeng
a45743c31e
Added main.py that now contains the One & Only Singleton instance of these classes:
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- Navigator
- Aplication
- Workflow
- Project
- Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.
2007-07-26 12:35:59 +00:00
Arnar Flatberg
939dba20ee
first import lpls
2007-07-23 17:35:28 +00:00
Einar Ryeng
7ea87e646a
Added DAG plot to gobrowser module and smokers workflow.
2007-07-23 17:02:28 +00:00
Arnar Flatberg
dd04e28a62
Query fix
2007-07-05 18:49:24 +00:00
Einar Ryeng
75c7c51708
DistanceToSelectionFunction
2007-07-05 18:36:59 +00:00
Einar Ryeng
3f5d45d7af
Renamed smalltest workflow to smokers.
2007-07-05 18:24:45 +00:00
Einar Ryeng
fae096afe4
Changed workflow name from smalltest to smokers, because it is heavily based
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on the smokers dataset.
2007-07-05 13:20:52 +00:00
Einar Ryeng
d29013a863
T-test now works, and outputs a histogram as well as t-values and p-values.
2007-07-03 16:25:38 +00:00
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
Arnar Flatberg