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
...
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:
...
* 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
...
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
...
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
...
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).
...
* 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
...
GTK/PyGTK, possibly due to PyGTK.
2009-02-06 22:24:33 +00:00
Einar Ryeng
648817cf0e
Removed debug print line.
2009-02-06 22:23:24 +00:00
Einar Ryeng
f07ce85e46
Changes to DAG plot.
2009-02-06 22:21:51 +00:00
Einar Ryeng
5cfa505ae2
Fixed critical bug in txt2ftsv that made output datasets incorrect if more than one list was used.
2009-02-06 22:21:19 +00:00
Einar Ryeng