einarr
dc8da8823e
Partial fix to #22 . Laydi will require a project directory to run. If the
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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
einarr
b5d2e8e181
Changed the name of the current Project class to ProjectView, to make room for a new
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non-GUI project class.
2011-03-06 22:33:51 +00:00
einarr
21133af8f7
Removing old r-laydi directory.
2011-03-06 21:27:36 +00:00
einarr
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
einarr
633465e4c8
* Added function fro reading laydi selections.
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* Fixed bug in documentation of write.laydi.selection.
2011-03-06 14:38:24 +00:00
einarr
6a70e7a4db
Removed old laydi.R
2011-03-06 14:32:37 +00:00
einarr
1d94b46777
Added method for writing laydi selections.
2011-03-05 16:28:07 +00:00
einarr
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
einarr
260e0ad715
First attemt on laydi R package.
2011-03-05 13:49:15 +00:00
einarr
80e64afd04
Renamed R package to R.
2011-03-04 14:25:33 +00:00
einarr
f18b49b1c7
R package for communicating with Laydi.
2011-03-04 14:24:55 +00:00
einarr
f29d48e879
Laydi project directory for testing the new project structure.
2011-01-12 16:57:10 +00:00
einarr
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
einarr
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
einarr
f001d12584
Working version.
2010-09-27 19:45:56 +00:00
einarr
3d68d27a56
Begun writing illumina data to ftsv converter.
2010-09-24 15:18:52 +00:00
einarr
b6d1eb022e
Fixes error during make in parent directory.
2010-06-30 08:30:15 +00:00
einarr
2e253450cd
Removed debug print statments.
2010-01-19 17:08:50 +00:00
einarr
259add178e
Removed matplotlibrc
2010-01-19 16:53:35 +00:00
einarr
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
einarr
c50d34effc
Changed from deprecated scipy.stats.mean() to numpy.mean().
2009-11-22 18:25:43 +00:00
einarr
f2afcbc3fc
Fixed description to run laydi after checkout.
2009-11-19 21:58:07 +00:00
einarr
1fbef303ff
Fixed warning about deprecated matplotlib setting.
2009-08-22 20:11:48 +00:00
einarr
e28b66a294
Removed annoying debug print statement.
2009-08-22 19:50:00 +00:00
einarr
58e7f6422b
Added build info in README
2009-08-22 19:48:20 +00:00
einarr
4ce6963428
Fixing selections and drawing in newer versions of matplotlib.
2009-08-22 17:41:06 +00:00
einarr
14de18c507
IMPORTANT: identifiers in the resulting csv file were not correct before this patch.
2009-02-28 15:38:29 +00:00
einarr
53cbd8fed7
Added write_csv function to export a dataset to regular comma/tab/whatever separated files.
2009-02-09 23:05:09 +00:00
einarr
0858fd00e5
ftsv2csv - script to convert ftsv files to comma/tab separated values.
2009-02-09 22:12:39 +00:00
einarr
a1e57d7820
Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions.
2009-02-06 23:48:25 +00:00
einarr
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
einarr
648817cf0e
Removed debug print line.
2009-02-06 22:23:24 +00:00
einarr
f07ce85e46
Changes to DAG plot.
2009-02-06 22:21:51 +00:00
einarr
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
einarr
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
einarr
b46c381c3e
Added txt2ftsv, a script to build ftsv category datasets from lists of identifiers.
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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
einarr
fdf51c7c7f
Added box and bar plots to the right-click menu of datasets.
2008-12-07 23:31:03 +00:00
einarr
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
einarr
2020c13b97
Fixing the colours of the overview image.
2008-12-06 14:37:10 +00:00
einarr
cc9416b3f7
GUI overview figure.
2008-12-06 00:58:35 +00:00
einarr
7e6bac20e1
FIXING STUFF!
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Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
einarr
1eabbc5c48
BREAKING STUFF!
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Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
einarr
9c026a39d0
BREAKING STUFF!
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Renaming from fluents to laydi
2008-12-05 21:50:32 +00:00
einarr
27e4504bf6
BREAKING STUFF!
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Rename fluents to laydi.
2008-12-05 21:48:24 +00:00
einarr
45a06fab7f
debian/rules builds a bit smoother by running configure with both --root and --prefix.
2008-12-05 20:03:02 +00:00
einarr
d3eba1cd8b
Deleted doc/Makefile because it should be generated by configure.
2008-12-05 20:02:13 +00:00
einarr
5739de0a61
Name change to Laydi.
2008-12-05 20:01:02 +00:00
einarr
444e524f44
Name cange to Laydi.
2008-12-05 19:59:55 +00:00
einarr
c544c983e4
Added --root to allow deb builds to go smoother.
2008-12-05 19:59:21 +00:00
einarr
04b7cbb872
Lots of changes in structure to make it possible to package the program while
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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
einarr