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
...
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
Arnar Flatberg