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  • d52dbbd9be Relocate wiki from trac main rot 2023-01-25 13:36:26 +0100
  • 36146893e6 Fixed selections. points_inside_poly is deprecated, and all calls are therefore rewritten to use Path.contains_points. Einar Ryeng 2014-04-04 19:16:59 +0000
  • 2b4da82165 Corrected URL to source code. Einar Ryeng 2013-10-17 08:24:43 +0000
  • c612724378 Fixed bug that caused right-click in the identifier list to change the list's selection status. Einar Ryeng 2013-09-17 11:11:13 +0000
  • 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__ Einar Ryeng 2012-01-25 18:13:54 +0000
  • 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. Einar Ryeng 2011-10-25 15:15:01 +0000
  • 660f649670 Some functions have been moved from scipy to numpy. Updated import statements to reflect this. Einar Ryeng 2011-10-21 22:04:11 +0000
  • d0f307c135 Removed debug print statements. Einar Ryeng 2011-07-07 13:11:12 +0000
  • 4ec79d2d9a Short code cleanup. Einar Ryeng 2011-06-02 15:14:21 +0000
  • 1845fe2ba0 Added rudimentary loading of annotation files. Einar Ryeng 2011-06-02 14:38:01 +0000
  • bad06e0bb9 Removed unused import of the dataset module. Einar Ryeng 2011-06-02 14:07:42 +0000
  • 5c65dc7e2c Removed old comments. Einar Ryeng 2011-06-02 13:22:25 +0000
  • 1c0ea0caee Automatically load all datasets in the root data directory and add them to navigator when project is loaded. Einar Ryeng 2011-06-02 13:16:10 +0000
  • e21cd7b323 More helpful error message if no project is specified. Einar Ryeng 2011-03-28 21:40:15 +0000
  • 6be624e872 Script to generate mapping files between identifiers found in tab separated files. Einar Ryeng 2011-03-24 08:46:17 +0000
  • f1b3009f11 Fixed a bug in the output Einar Ryeng 2011-03-24 08:05:49 +0000
  • 19163988e3 Example project. Einar Ryeng 2011-03-17 10:49:08 +0000
  • 11fc34b1e3 Fixes #23 - Preserving the order of samples in subdata. Einar Ryeng 2011-03-08 09:27:06 +0000
  • ed486ddf2e Changed default directories for: * Load dataset * Import annotations * Export annotations to the correct directories in the current project. Einar Ryeng 2011-03-07 16:19:45 +0000
  • ec71cbd7d7 Fixes previous broken commit. Einar Ryeng 2011-03-06 23:11:29 +0000
  • 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> }}} Einar Ryeng 2011-03-06 23:08:09 +0000
  • b5d2e8e181 Changed the name of the current Project class to ProjectView, to make room for a new non-GUI project class. Einar Ryeng 2011-03-06 22:33:51 +0000
  • 21133af8f7 Removing old r-laydi directory. Einar Ryeng 2011-03-06 21:27:36 +0000
  • a1ab79024e Adding simple workflow named "default" with PCA, PLS and LPLS. Changed the program to use this as the default workflow. Einar Ryeng 2011-03-06 15:27:16 +0000
  • 633465e4c8 * Added function fro reading laydi selections. * Fixed bug in documentation of write.laydi.selection. Einar Ryeng 2011-03-06 14:38:24 +0000
  • 6a70e7a4db Removed old laydi.R Einar Ryeng 2011-03-06 14:32:37 +0000
  • 1d94b46777 Added method for writing laydi selections. Einar Ryeng 2011-03-05 16:28:07 +0000
  • 98a9d581af Updated R package. The package now works and is documented. The only implemented method is writing ftsv datasets from R. Einar Ryeng 2011-03-05 15:47:33 +0000
  • 260e0ad715 First attemt on laydi R package. Einar Ryeng 2011-03-05 13:49:15 +0000
  • 80e64afd04 Renamed R package to R. Einar Ryeng 2011-03-04 14:25:33 +0000
  • f18b49b1c7 R package for communicating with Laydi. Einar Ryeng 2011-03-04 14:24:55 +0000
  • f29d48e879 Laydi project directory for testing the new project structure. Einar Ryeng 2011-01-12 16:57:10 +0000
  • ebda69049e Started working on Dimension and Universe objects (which will probably be renamed before actually being used in the program). Einar Ryeng 2011-01-05 15:48:00 +0000
  • 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. Einar Ryeng 2011-01-04 11:43:24 +0000
  • f001d12584 Working version. Einar Ryeng 2010-09-27 19:45:56 +0000
  • 3d68d27a56 Begun writing illumina data to ftsv converter. Einar Ryeng 2010-09-24 15:18:52 +0000
  • b6d1eb022e Fixes error during make in parent directory. Einar Ryeng 2010-06-30 08:30:15 +0000
  • 2e253450cd Removed debug print statments. Einar Ryeng 2010-01-19 17:08:50 +0000
  • 259add178e Removed matplotlibrc Einar Ryeng 2010-01-19 16:53:35 +0000
  • 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. Einar Ryeng 2010-01-19 16:45:51 +0000
  • c50d34effc Changed from deprecated scipy.stats.mean() to numpy.mean(). Einar Ryeng 2009-11-22 18:25:43 +0000
  • f2afcbc3fc Fixed description to run laydi after checkout. Einar Ryeng 2009-11-19 21:58:07 +0000
  • 1fbef303ff Fixed warning about deprecated matplotlib setting. Einar Ryeng 2009-08-22 20:11:48 +0000
  • e28b66a294 Removed annoying debug print statement. Einar Ryeng 2009-08-22 19:50:00 +0000
  • 58e7f6422b Added build info in README Einar Ryeng 2009-08-22 19:48:20 +0000
  • 4ce6963428 Fixing selections and drawing in newer versions of matplotlib. Einar Ryeng 2009-08-22 17:41:06 +0000
  • 14de18c507 IMPORTANT: identifiers in the resulting csv file were not correct before this patch. Einar Ryeng 2009-02-28 15:38:29 +0000
  • 53cbd8fed7 Added write_csv function to export a dataset to regular comma/tab/whatever separated files. Einar Ryeng 2009-02-09 23:05:09 +0000
  • 0858fd00e5 ftsv2csv - script to convert ftsv files to comma/tab separated values. Einar Ryeng 2009-02-09 22:12:39 +0000
  • a1e57d7820 Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions. Einar Ryeng 2009-02-06 23:48:25 +0000
  • 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. Einar Ryeng 2009-02-06 22:24:33 +0000
  • 648817cf0e Removed debug print line. Einar Ryeng 2009-02-06 22:23:24 +0000
  • f07ce85e46 Changes to DAG plot. Einar Ryeng 2009-02-06 22:21:51 +0000
  • 5cfa505ae2 Fixed critical bug in txt2ftsv that made output datasets incorrect if more than one list was used. Einar Ryeng 2009-02-06 22:21:19 +0000
  • 6c20de11c9 Added options to txt2ftsv to chose between datasets and category datasets and whether or not to use sparse format. Einar Ryeng 2009-02-05 20:08:51 +0000
  • 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. Einar Ryeng 2009-02-05 00:11:48 +0000
  • fdf51c7c7f Added box and bar plots to the right-click menu of datasets. Einar Ryeng 2008-12-07 23:31:03 +0000
  • 0a76e9c50f Made plot background color lighter and removed two parameters that newer versions of matplotlib does not recognize. Einar Ryeng 2008-12-07 23:30:33 +0000
  • 2020c13b97 Fixing the colours of the overview image. Einar Ryeng 2008-12-06 14:37:10 +0000
  • cc9416b3f7 GUI overview figure. Einar Ryeng 2008-12-06 00:58:35 +0000
  • 7e6bac20e1 FIXING STUFF! Rename should be complete or almost so. Einar Ryeng 2008-12-05 22:07:56 +0000
  • 1eabbc5c48 BREAKING STUFF! Renaming fluents to laydi Einar Ryeng 2008-12-05 21:51:08 +0000
  • 9c026a39d0 BREAKING STUFF! Renaming from fluents to laydi Einar Ryeng 2008-12-05 21:50:32 +0000
  • 27e4504bf6 BREAKING STUFF! Einar Ryeng 2008-12-05 21:48:24 +0000
  • 45a06fab7f debian/rules builds a bit smoother by running configure with both --root and --prefix. Einar Ryeng 2008-12-05 20:03:02 +0000
  • d3eba1cd8b Deleted doc/Makefile because it should be generated by configure. Einar Ryeng 2008-12-05 20:02:13 +0000
  • 5739de0a61 Name change to Laydi. Einar Ryeng 2008-12-05 20:01:02 +0000
  • 444e524f44 Name cange to Laydi. Einar Ryeng 2008-12-05 19:59:55 +0000
  • c544c983e4 Added --root to allow deb builds to go smoother. Einar Ryeng 2008-12-05 19:59:21 +0000
  • 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. Einar Ryeng 2008-12-05 00:12:49 +0000
  • b313cf29bc Workflow updates Arnar Flatberg 2008-02-29 16:23:57 +0000
  • 1ad8b1a4f1 Fixed initial settings of axis in scatter Arnar Flatberg 2008-02-29 16:16:17 +0000
  • aa3ec28ec6 Switched hard-coded 3-s with a variable to determine size of viewport resizing dialog on toolbar. Einar Ryeng 2008-02-27 17:38:01 +0000
  • cb6d6b87cc Whatnot Arnar Flatberg 2008-02-08 14:58:46 +0000
  • 6b78629946 Save identifier list. Einar Ryeng 2008-02-07 18:15:39 +0000
  • a380093afc Added workflowdir to configuration file. workflowdir is a semicolon separated path of directories where workflows can be found. Einar Ryeng 2008-02-07 14:20:52 +0000
  • e6a671a8c0 Added function to split datasets on selection. Einar Ryeng 2008-02-06 19:54:17 +0000
  • b37ebe568f Fixed subdata method so the correct identifiers are stored Arnar Flatberg 2008-02-06 16:29:02 +0000
  • e417547923 cc Arnar Flatberg 2008-02-06 09:42:46 +0000
  • 14d24d02c2 Demo workflow Arnar Flatberg 2008-02-05 11:34:14 +0000
  • 848ba7f80c Added drag-n-drop of matrices to idlist window to support ranking of selected variables. Einar Ryeng 2008-02-01 11:09:10 +0000
  • f83a16ec37 Added new script. Einar Ryeng 2008-01-21 11:15:54 +0000
  • 9e4f86c557 Fixed writing of nodepos to assert ds type + added subdata function Arnar Flatberg 2008-01-15 11:41:53 +0000
  • 56a572c4ee Removed unnecessary line from from_networkx. Einar Ryeng 2008-01-08 10:19:57 +0000
  • ab9c1ec84b Sparse network support and nodepos read/write Arnar Flatberg 2008-01-08 00:43:56 +0000
  • bf29661af9 Added convertion to sparse format in category dataset Arnar Flatberg 2008-01-07 13:13:27 +0000
  • e6625c975f bugfix Arnar Flatberg 2008-01-07 12:44:08 +0000
  • ca267920d8 Removed a couple of output datasets that did not work from pls. Einar Ryeng 2008-01-07 10:47:17 +0000
  • bed280353b Added support for sparse category-dataset Arnar Flatberg 2008-01-06 17:01:00 +0000
  • a84731da30 Support for icon assignment based on introspection Arnar Flatberg 2007-12-17 18:52:49 +0000
  • 163271fc17 Correct behavior of dataset icons and names under transformations Arnar Flatberg 2007-12-17 18:50:27 +0000
  • 083702b3b1 Fixed bug in color updating Arnar Flatberg 2007-12-15 14:50:33 +0000
  • e80440472d Fixed axes scaling error in scatterplot Arnar Flatberg 2007-12-14 17:27:12 +0000
  • 4de9a58ae9 Made a LoadDataFunction instead of four almost identical specialiced Funcions. Einar Ryeng 2007-12-14 16:45:05 +0000
  • 07477888bb Fixed colormap bug Arnar Flatberg 2007-12-14 15:43:35 +0000
  • 5c2df5c163 Removed get_project nonsense Arnar Flatberg 2007-12-14 15:42:37 +0000
  • 6996aab2fa Added log transform, support for multi selections in navigator-scatter, removed get_project-nonsense Arnar Flatberg 2007-12-14 15:42:17 +0000
  • a94c3ed1cc Smoker workflow now loads data from correct path. Einar Ryeng 2007-12-14 15:15:01 +0000
  • 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. Einar Ryeng 2007-12-14 11:48:21 +0000
  • 0e8d864ace Does not need to import workflows. Einar Ryeng 2007-12-14 11:46:08 +0000