36146893e6
Fixed selections. points_inside_poly is deprecated, and all calls are therefore rewritten to use Path.contains_points.
einarr2014-04-04 19:16:59 +00:00
2b4da82165
Corrected URL to source code.
einarr2013-10-17 08:24:43 +00:00
c612724378
Fixed bug that caused right-click in the identifier list to change the list's selection status.
einarr2013-09-17 11:11:13 +00:00
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__
einarr2012-01-25 18:13:54 +00:00
4dcbff3647
Added reference to Selector objects to avoid the object from going to GC. This change is triggered by changes to mpl, but should not break with old versions.
einarr2011-10-25 15:15:01 +00:00
660f649670
Some functions have been moved from scipy to numpy. Updated import statements to reflect this.
einarr2011-10-21 22:04:11 +00:00
1845fe2ba0
Added rudimentary loading of annotation files.
einarr2011-06-02 14:38:01 +00:00
bad06e0bb9
Removed unused import of the dataset module.
einarr2011-06-02 14:07:42 +00:00
5c65dc7e2c
Removed old comments.
einarr2011-06-02 13:22:25 +00:00
1c0ea0caee
Automatically load all datasets in the root data directory and add them to navigator when project is loaded.
einarr2011-06-02 13:16:10 +00:00
e21cd7b323
More helpful error message if no project is specified.
einarr2011-03-28 21:40:15 +00:00
6be624e872
Script to generate mapping files between identifiers found in tab separated files.
einarr2011-03-24 08:46:17 +00:00
f1b3009f11
Fixed a bug in the output
einarr2011-03-24 08:05:49 +00:00
11fc34b1e3Fixes#23 - Preserving the order of samples in subdata.
einarr2011-03-08 09:27:06 +00:00
ed486ddf2e
Changed default directories for: * Load dataset * Import annotations * Export annotations to the correct directories in the current project.
einarr2011-03-07 16:19:45 +00:00
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> }}}
einarr2011-03-06 23:08:09 +00:00
b5d2e8e181
Changed the name of the current Project class to ProjectView, to make room for a new non-GUI project class.
einarr2011-03-06 22:33:51 +00:00
21133af8f7
Removing old r-laydi directory.
einarr2011-03-06 21:27:36 +00:00
a1ab79024e
Adding simple workflow named "default" with PCA, PLS and LPLS. Changed the program to use this as the default workflow.
einarr2011-03-06 15:27:16 +00:00
633465e4c8
* Added function fro reading laydi selections. * Fixed bug in documentation of write.laydi.selection.
einarr2011-03-06 14:38:24 +00:00
1d94b46777
Added method for writing laydi selections.
einarr2011-03-05 16:28:07 +00:00
98a9d581af
Updated R package. The package now works and is documented. The only implemented method is writing ftsv datasets from R.
einarr2011-03-05 15:47:33 +00:00
260e0ad715
First attemt on laydi R package.
einarr2011-03-05 13:49:15 +00:00
80e64afd04
Renamed R package to R.
einarr2011-03-04 14:25:33 +00:00
f18b49b1c7
R package for communicating with Laydi.
einarr2011-03-04 14:24:55 +00:00
f29d48e879
Laydi project directory for testing the new project structure.
einarr2011-01-12 16:57:10 +00:00
ebda69049e
Started working on Dimension and Universe objects (which will probably be renamed before actually being used in the program).
einarr2011-01-05 15:48:00 +00:00
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.
einarr2011-01-04 11:43:24 +00:00
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.
einarr2010-01-19 16:45:51 +00:00
c50d34effc
Changed from deprecated scipy.stats.mean() to numpy.mean().
einarr2009-11-22 18:25:43 +00:00
f2afcbc3fc
Fixed description to run laydi after checkout.
einarr2009-11-19 21:58:07 +00:00
1fbef303ff
Fixed warning about deprecated matplotlib setting.
einarr2009-08-22 20:11:48 +00:00
58e7f6422b
Added build info in README
einarr2009-08-22 19:48:20 +00:00
4ce6963428
Fixing selections and drawing in newer versions of matplotlib.
einarr2009-08-22 17:41:06 +00:00
14de18c507
IMPORTANT: identifiers in the resulting csv file were not correct before this patch.
einarr2009-02-28 15:38:29 +00:00
53cbd8fed7
Added write_csv function to export a dataset to regular comma/tab/whatever separated files.
einarr2009-02-09 23:05:09 +00:00
0858fd00e5
ftsv2csv - script to convert ftsv files to comma/tab separated values.
einarr2009-02-09 22:12:39 +00:00
a1e57d7820
Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions.
einarr2009-02-06 23:48:25 +00:00
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.
einarr2009-02-06 22:24:33 +00:00
f07ce85e46
Changes to DAG plot.
einarr2009-02-06 22:21:51 +00:00
5cfa505ae2
Fixed critical bug in txt2ftsv that made output datasets incorrect if more than one list was used.
einarr2009-02-06 22:21:19 +00:00
6c20de11c9
Added options to txt2ftsv to chose between datasets and category datasets and whether or not to use sparse format.
einarr2009-02-05 20:08:51 +00:00
b46c381c3e
Added txt2ftsv, a script to build ftsv category datasets from lists of identifiers. Usages is txt2ftsv [-d dimension] [-o output.ftsv] [-n dsname] [FILE1 [FILE2 ...]] Input and output can be - for STDIN/STDOUT respectively. The script is primarily ment as a hack to easily load selections. Data is only half sanitized.
einarr2009-02-05 00:11:48 +00:00
fdf51c7c7f
Added box and bar plots to the right-click menu of datasets.
einarr2008-12-07 23:31:03 +00:00
0a76e9c50f
Made plot background color lighter and removed two parameters that newer versions of matplotlib does not recognize.
einarr2008-12-07 23:30:33 +00:00
2020c13b97
Fixing the colours of the overview image.
einarr2008-12-06 14:37:10 +00:00
45a06fab7f
debian/rules builds a bit smoother by running configure with both --root and --prefix.
einarr2008-12-05 20:03:02 +00:00
d3eba1cd8b
Deleted doc/Makefile because it should be generated by configure.
einarr2008-12-05 20:02:13 +00:00
5739de0a61
Name change to Laydi.
einarr2008-12-05 20:01:02 +00:00
444e524f44
Name cange to Laydi.
einarr2008-12-05 19:59:55 +00:00
c544c983e4
Added --root to allow deb builds to go smoother.
einarr2008-12-05 19:59:21 +00:00
04b7cbb872
Lots of changes in structure to make it possible to package the program while still allowing workflows to be placed in several locations in the file system.
einarr2008-12-05 00:12:49 +00:00
6b78629946
Save identifier list.
einarr2008-02-07 18:15:39 +00:00
a380093afc
Added workflowdir to configuration file. workflowdir is a semicolon separated path of directories where workflows can be found.
einarr2008-02-07 14:20:52 +00:00
e6a671a8c0
Added function to split datasets on selection.
einarr2008-02-06 19:54:17 +00:00
b37ebe568f
Fixed subdata method so the correct identifiers are stored
flatberg2008-02-06 16:29:02 +00:00
6996aab2fa
Added log transform, support for multi selections in navigator-scatter, removed get_project-nonsense
flatberg2007-12-14 15:42:17 +00:00
a94c3ed1cc
Smoker workflow now loads data from correct path.
einarr2007-12-14 15:15:01 +00:00
ba7d8fc34f
Changed the way workflows are handled. You now specify a workflow by naming the containing python module. The module must be in python's path.
einarr2007-12-14 11:48:21 +00:00
0e8d864ace
Does not need to import workflows.
einarr2007-12-14 11:46:08 +00:00
drift
einarr
flatberg