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:
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* 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
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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
Einar Ryeng
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
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
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use this as the default workflow.
2011-03-06 15:27:16 +00:00
Einar Ryeng
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
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
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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
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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
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).
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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
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
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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.
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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
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!
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Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
Einar Ryeng
1eabbc5c48
BREAKING STUFF!
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Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
Einar Ryeng
9c026a39d0
BREAKING STUFF!
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Renaming from fluents to laydi
2008-12-05 21:50:32 +00:00
Einar Ryeng
27e4504bf6
BREAKING STUFF!
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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