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557 Commits

Author SHA1 Message Date
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 6c20de11c9 Added options to txt2ftsv to chose between datasets and category datasets and whether or not to use sparse format. 2009-02-05 20:08:51 +00:00
Einar Ryeng 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.
2009-02-05 00:11:48 +00:00
Einar Ryeng fdf51c7c7f Added box and bar plots to the right-click menu of datasets. 2008-12-07 23:31:03 +00:00
Einar Ryeng 0a76e9c50f Made plot background color lighter and removed two parameters that newer versions of matplotlib does not recognize. 2008-12-07 23:30:33 +00:00
Einar Ryeng 2020c13b97 Fixing the colours of the overview image. 2008-12-06 14:37:10 +00:00
Einar Ryeng cc9416b3f7 GUI overview figure. 2008-12-06 00:58:35 +00:00
Einar Ryeng 7e6bac20e1 FIXING STUFF!
Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
Einar Ryeng 1eabbc5c48 BREAKING STUFF!
Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
Einar Ryeng 9c026a39d0 BREAKING STUFF!
Renaming from fluents to laydi
2008-12-05 21:50:32 +00:00
Einar Ryeng 27e4504bf6 BREAKING STUFF!
Rename fluents to laydi.
2008-12-05 21:48:24 +00:00
Einar Ryeng 45a06fab7f debian/rules builds a bit smoother by running configure with both --root and --prefix. 2008-12-05 20:03:02 +00:00
Einar Ryeng d3eba1cd8b Deleted doc/Makefile because it should be generated by configure. 2008-12-05 20:02:13 +00:00
Einar Ryeng 5739de0a61 Name change to Laydi. 2008-12-05 20:01:02 +00:00
Einar Ryeng 444e524f44 Name cange to Laydi. 2008-12-05 19:59:55 +00:00
Einar Ryeng c544c983e4 Added --root to allow deb builds to go smoother. 2008-12-05 19:59:21 +00:00
Einar Ryeng 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.

The installation procedure is now ./configure && make install configure will
run m4 on fluents/paths.py.m4, Makefile.m4 and doc/Makefile.m4 so that the
installation system and the program will know where some important directories
are located.

The paths.py.m4 and consequently also pahts.py files are just listings of
directories configured during install.  I did this to separate these from all
other files so that as little as possible is touched by m4. It is still
necessary to do an install now to get the program to run in a clean checkout.

Workflows can now be placed anywhere in the system. This is done by setting the
workflowdir variable in the configuration file. All workflow directories,
separated by semicolons, are added to the python path.

The use of setup.py is now deprecated.
2008-12-05 00:12:49 +00:00
Arnar Flatberg b313cf29bc Workflow updates 2008-02-29 16:23:57 +00:00
Arnar Flatberg 1ad8b1a4f1 Fixed initial settings of axis in scatter 2008-02-29 16:16:17 +00:00
Einar Ryeng aa3ec28ec6 Switched hard-coded 3-s with a variable to determine size of viewport resizing
dialog on toolbar.
2008-02-27 17:38:01 +00:00