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
...
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
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
Truls Alexander Tangstad
a2d3a9d5cc
Made PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input.
2006-04-28 11:44:55 +00:00
Truls Alexander Tangstad
8fd1f4ba83
Renamed module for affy workflow.
2006-04-27 15:06:01 +00:00
Einar Ryeng
0df56248ee
Removed obsolete module annotations.
2006-04-27 12:41:51 +00:00
Truls Alexander Tangstad
fe0cf736f5
Created affy workflow.
2006-04-27 12:15:30 +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
Arnar Flatberg
cfbb76f25a
import * removed
2006-04-24 16:05:54 +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
cebf801cf6
bugix on creation of output data (E) from pca
2006-04-24 12:51:43 +00:00
Einar Ryeng
Arnar Flatberg
Truls Alexander Tangstad
Reidar Strand Hagen