Einar Ryeng
36146893e6
Fixed selections. points_inside_poly is deprecated, and all calls are therefore
...
rewritten to use Path.contains_points.
2014-04-04 19:16:59 +00:00
Einar Ryeng
2b4da82165
Corrected URL to source code.
2013-10-17 08:24:43 +00:00
Einar Ryeng
c612724378
Fixed bug that caused right-click in the identifier list to change the list's selection status.
2013-09-17 11:11:13 +00:00
Einar Ryeng
1f2055d6b7
* Added selection directories. The selection/ directory in a project
...
should contain subdirectories per dimension. Selections are files within
these subdirectories ending in .sel
* Renamed Universe.__getent__ to Universe.__getitem__
2012-01-25 18:13:54 +00:00
Einar Ryeng
4dcbff3647
Added reference to Selector objects to avoid the object from going to GC.
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This change is triggered by changes to mpl, but should not break with
old versions.
2011-10-25 15:15:01 +00:00
Einar Ryeng
660f649670
Some functions have been moved from scipy to numpy. Updated import statements to reflect this.
2011-10-21 22:04:11 +00:00
Einar Ryeng
d0f307c135
Removed debug print statements.
2011-07-07 13:11:12 +00:00
Einar Ryeng
4ec79d2d9a
Short code cleanup.
2011-06-02 15:14:21 +00:00
Einar Ryeng
1845fe2ba0
Added rudimentary loading of annotation files.
2011-06-02 14:38:01 +00:00
Einar Ryeng
bad06e0bb9
Removed unused import of the dataset module.
2011-06-02 14:07:42 +00:00
Einar Ryeng
5c65dc7e2c
Removed old comments.
2011-06-02 13:22:25 +00:00
Einar Ryeng
1c0ea0caee
Automatically load all datasets in the root data directory and add them to
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navigator when project is loaded.
Recursion down in data hierarchy is not yet implemented.
2011-06-02 13:16:10 +00:00
Einar Ryeng
e21cd7b323
More helpful error message if no project is specified.
2011-03-28 21:40:15 +00:00
Einar Ryeng
6be624e872
Script to generate mapping files between identifiers found in tab separated files.
2011-03-24 08:46:17 +00:00
Einar Ryeng
f1b3009f11
Fixed a bug in the output
2011-03-24 08:05:49 +00:00
Einar Ryeng
19163988e3
Example project.
2011-03-17 10:49:08 +00:00
Einar Ryeng
11fc34b1e3
Fixes #23 - Preserving the order of samples in subdata.
2011-03-08 09:27:06 +00:00
Einar Ryeng
ed486ddf2e
Changed default directories for:
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* Load dataset
* Import annotations
* Export annotations
to the correct directories in the current project.
2011-03-07 16:19:45 +00:00
Einar Ryeng
ec71cbd7d7
Fixes previous broken commit.
2011-03-06 23:11:29 +00:00
Einar Ryeng
dc8da8823e
Partial fix to #22 . Laydi will require a project directory to run. If the
...
project directory does not exist, i.e. if a new project should be created, the
new -n switch is required. New syntax to run laydi is now
{{{
laydi [options] </path/to/project>
}}}
2011-03-06 23:08:09 +00:00
Einar Ryeng
b5d2e8e181
Changed the name of the current Project class to ProjectView, to make room for a new
...
non-GUI project class.
2011-03-06 22:33:51 +00:00
Einar Ryeng
21133af8f7
Removing old r-laydi directory.
2011-03-06 21:27:36 +00:00
Einar Ryeng
a1ab79024e
Adding simple workflow named "default" with PCA, PLS and LPLS. Changed the program to
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use this as the default workflow.
2011-03-06 15:27:16 +00:00
Einar Ryeng
633465e4c8
* Added function fro reading laydi selections.
...
* Fixed bug in documentation of write.laydi.selection.
2011-03-06 14:38:24 +00:00
Einar Ryeng
6a70e7a4db
Removed old laydi.R
2011-03-06 14:32:37 +00:00
Einar Ryeng
1d94b46777
Added method for writing laydi selections.
2011-03-05 16:28:07 +00:00
Einar Ryeng
98a9d581af
Updated R package. The package now works and is documented. The only implemented
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method is writing ftsv datasets from R.
2011-03-05 15:47:33 +00:00
Einar Ryeng
260e0ad715
First attemt on laydi R package.
2011-03-05 13:49:15 +00:00
Einar Ryeng
80e64afd04
Renamed R package to R.
2011-03-04 14:25:33 +00:00
Einar Ryeng
f18b49b1c7
R package for communicating with Laydi.
2011-03-04 14:24:55 +00:00
Einar Ryeng
f29d48e879
Laydi project directory for testing the new project structure.
2011-01-12 16:57:10 +00:00
Einar Ryeng
ebda69049e
Started working on Dimension and Universe objects (which will probably be renamed before actually being used in the program).
2011-01-05 15:48:00 +00:00
Einar Ryeng
5f1f4d0dc2
Renamed directory illumina2ftsv to illumina to gather all Illumina-relevant
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scripts there. Added laydi-annot-illumina script that generates Laydi
annotation files from Illumina text annotation files.
2011-01-04 11:43:24 +00:00
Einar Ryeng
f001d12584
Working version.
2010-09-27 19:45:56 +00:00
Einar Ryeng
3d68d27a56
Begun writing illumina data to ftsv converter.
2010-09-24 15:18:52 +00:00
Einar Ryeng
b6d1eb022e
Fixes error during make in parent directory.
2010-06-30 08:30:15 +00:00
Einar Ryeng
2e253450cd
Removed debug print statments.
2010-01-19 17:08:50 +00:00
Einar Ryeng
259add178e
Removed matplotlibrc
2010-01-19 16:53:35 +00:00
Einar Ryeng
256133275c
* Changed build behaviour to suit newer Ubuntu releases (at least 9.10).
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* Added -c option to generate intial configuration file and directories. This will create
the file ~/.laydi and the directories ~/laydi/datasets and ~/laydi/workflows.
* Removed debug print statements.
2010-01-19 16:45:51 +00:00
Einar Ryeng
c50d34effc
Changed from deprecated scipy.stats.mean() to numpy.mean().
2009-11-22 18:25:43 +00:00
Einar Ryeng
f2afcbc3fc
Fixed description to run laydi after checkout.
2009-11-19 21:58:07 +00:00
Einar Ryeng
1fbef303ff
Fixed warning about deprecated matplotlib setting.
2009-08-22 20:11:48 +00:00
Einar Ryeng
e28b66a294
Removed annoying debug print statement.
2009-08-22 19:50:00 +00:00
Einar Ryeng
58e7f6422b
Added build info in README
2009-08-22 19:48:20 +00:00
Einar Ryeng
4ce6963428
Fixing selections and drawing in newer versions of matplotlib.
2009-08-22 17:41:06 +00:00
Einar Ryeng
14de18c507
IMPORTANT: identifiers in the resulting csv file were not correct before this patch.
2009-02-28 15:38:29 +00:00
Einar Ryeng
53cbd8fed7
Added write_csv function to export a dataset to regular comma/tab/whatever separated files.
2009-02-09 23:05:09 +00:00
Einar Ryeng
0858fd00e5
ftsv2csv - script to convert ftsv files to comma/tab separated values.
2009-02-09 22:12:39 +00:00
Einar Ryeng
a1e57d7820
Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions.
2009-02-06 23:48:25 +00:00
Einar Ryeng
ec6f2a1edc
Removed page size from spin boxes as this has become deprecated in GTK. There are still complaints from
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GTK/PyGTK, possibly due to PyGTK.
2009-02-06 22:24:33 +00:00
Einar Ryeng