d52dbbd9be
Relocate wiki from trac
2023-01-25 13:36:26 +01:00
36146893e6
Fixed selections. points_inside_poly is deprecated, and all calls are therefore
...
rewritten to use Path.contains_points.
2014-04-04 19:16:59 +00:00
2b4da82165
Corrected URL to source code.
2013-10-17 08:24:43 +00:00
c612724378
Fixed bug that caused right-click in the identifier list to change the list's selection status.
2013-09-17 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__
2012-01-25 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.
2011-10-25 15:15:01 +00:00
660f649670
Some functions have been moved from scipy to numpy. Updated import statements to reflect this.
2011-10-21 22:04:11 +00:00
d0f307c135
Removed debug print statements.
2011-07-07 13:11:12 +00:00
4ec79d2d9a
Short code cleanup.
2011-06-02 15:14:21 +00:00
1845fe2ba0
Added rudimentary loading of annotation files.
2011-06-02 14:38:01 +00:00
bad06e0bb9
Removed unused import of the dataset module.
2011-06-02 14:07:42 +00:00
5c65dc7e2c
Removed old comments.
2011-06-02 13:22:25 +00:00
1c0ea0caee
Automatically load all datasets in the root data directory and add them to
...
navigator when project is loaded.
Recursion down in data hierarchy is not yet implemented.
2011-06-02 13:16:10 +00:00
e21cd7b323
More helpful error message if no project is specified.
2011-03-28 21:40:15 +00:00
6be624e872
Script to generate mapping files between identifiers found in tab separated files.
2011-03-24 08:46:17 +00:00
f1b3009f11
Fixed a bug in the output
2011-03-24 08:05:49 +00:00
19163988e3
Example project.
2011-03-17 10:49:08 +00:00
11fc34b1e3
Fixes #23 - Preserving the order of samples in subdata.
2011-03-08 09:27:06 +00:00
ed486ddf2e
Changed default directories for:
...
* Load dataset
* Import annotations
* Export annotations
to the correct directories in the current project.
2011-03-07 16:19:45 +00:00
ec71cbd7d7
Fixes previous broken commit.
2011-03-06 23:11:29 +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>
}}}
2011-03-06 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.
2011-03-06 22:33:51 +00:00
21133af8f7
Removing old r-laydi directory.
2011-03-06 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.
2011-03-06 15:27:16 +00:00
633465e4c8
* Added function fro reading laydi selections.
...
* Fixed bug in documentation of write.laydi.selection.
2011-03-06 14:38:24 +00:00
6a70e7a4db
Removed old laydi.R
2011-03-06 14:32:37 +00:00
1d94b46777
Added method for writing laydi selections.
2011-03-05 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.
2011-03-05 15:47:33 +00:00
260e0ad715
First attemt on laydi R package.
2011-03-05 13:49:15 +00:00
80e64afd04
Renamed R package to R.
2011-03-04 14:25:33 +00:00
f18b49b1c7
R package for communicating with Laydi.
2011-03-04 14:24:55 +00:00
f29d48e879
Laydi project directory for testing the new project structure.
2011-01-12 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).
2011-01-05 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.
2011-01-04 11:43:24 +00:00
f001d12584
Working version.
2010-09-27 19:45:56 +00:00
3d68d27a56
Begun writing illumina data to ftsv converter.
2010-09-24 15:18:52 +00:00
b6d1eb022e
Fixes error during make in parent directory.
2010-06-30 08:30:15 +00:00
2e253450cd
Removed debug print statments.
2010-01-19 17:08:50 +00:00
259add178e
Removed matplotlibrc
2010-01-19 16:53:35 +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.
2010-01-19 16:45:51 +00:00
c50d34effc
Changed from deprecated scipy.stats.mean() to numpy.mean().
2009-11-22 18:25:43 +00:00
f2afcbc3fc
Fixed description to run laydi after checkout.
2009-11-19 21:58:07 +00:00
1fbef303ff
Fixed warning about deprecated matplotlib setting.
2009-08-22 20:11:48 +00:00
e28b66a294
Removed annoying debug print statement.
2009-08-22 19:50:00 +00:00
58e7f6422b
Added build info in README
2009-08-22 19:48:20 +00:00
4ce6963428
Fixing selections and drawing in newer versions of matplotlib.
2009-08-22 17:41:06 +00:00
14de18c507
IMPORTANT: identifiers in the resulting csv file were not correct before this patch.
2009-02-28 15:38:29 +00:00
53cbd8fed7
Added write_csv function to export a dataset to regular comma/tab/whatever separated files.
2009-02-09 23:05:09 +00:00
0858fd00e5
ftsv2csv - script to convert ftsv files to comma/tab separated values.
2009-02-09 22:12:39 +00:00
a1e57d7820
Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions.
2009-02-06 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.
2009-02-06 22:24:33 +00:00
648817cf0e
Removed debug print line.
2009-02-06 22:23:24 +00:00
f07ce85e46
Changes to DAG plot.
2009-02-06 22:21:51 +00:00
5cfa505ae2
Fixed critical bug in txt2ftsv that made output datasets incorrect if more than one list was used.
2009-02-06 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.
2009-02-05 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.
2009-02-05 00:11:48 +00:00
fdf51c7c7f
Added box and bar plots to the right-click menu of datasets.
2008-12-07 23:31:03 +00:00
0a76e9c50f
Made plot background color lighter and removed two parameters that newer versions of matplotlib does not recognize.
2008-12-07 23:30:33 +00:00
2020c13b97
Fixing the colours of the overview image.
2008-12-06 14:37:10 +00:00
cc9416b3f7
GUI overview figure.
2008-12-06 00:58:35 +00:00
7e6bac20e1
FIXING STUFF!
...
Rename should be complete or almost so.
2008-12-05 22:07:56 +00:00
1eabbc5c48
BREAKING STUFF!
...
Renaming fluents to laydi
2008-12-05 21:51:08 +00:00
9c026a39d0
BREAKING STUFF!
...
Renaming from fluents to laydi
2008-12-05 21:50:32 +00:00
27e4504bf6
BREAKING STUFF!
...
Rename fluents to laydi.
2008-12-05 21:48:24 +00:00
45a06fab7f
debian/rules builds a bit smoother by running configure with both --root and --prefix.
2008-12-05 20:03:02 +00:00
d3eba1cd8b
Deleted doc/Makefile because it should be generated by configure.
2008-12-05 20:02:13 +00:00
5739de0a61
Name change to Laydi.
2008-12-05 20:01:02 +00:00
444e524f44
Name cange to Laydi.
2008-12-05 19:59:55 +00:00
c544c983e4
Added --root to allow deb builds to go smoother.
2008-12-05 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.
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
b313cf29bc
Workflow updates
2008-02-29 16:23:57 +00:00
1ad8b1a4f1
Fixed initial settings of axis in scatter
2008-02-29 16:16:17 +00:00
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
cb6d6b87cc
Whatnot
2008-02-08 14:58:46 +00:00
6b78629946
Save identifier list.
2008-02-07 18:15:39 +00:00
a380093afc
Added workflowdir to configuration file. workflowdir is a semicolon separated
...
path of directories where workflows can be found.
2008-02-07 14:20:52 +00:00
e6a671a8c0
Added function to split datasets on selection.
2008-02-06 19:54:17 +00:00
b37ebe568f
Fixed subdata method so the correct identifiers are stored
2008-02-06 16:29:02 +00:00
e417547923
cc
2008-02-06 09:42:46 +00:00
14d24d02c2
Demo workflow
2008-02-05 11:34:14 +00:00
848ba7f80c
Added drag-n-drop of matrices to idlist window to support ranking of selected variables.
2008-02-01 11:09:10 +00:00
f83a16ec37
Added new script.
2008-01-21 11:15:54 +00:00
9e4f86c557
Fixed writing of nodepos to assert ds type + added subdata function
2008-01-15 11:41:53 +00:00
56a572c4ee
Removed unnecessary line from from_networkx.
2008-01-08 10:19:57 +00:00
ab9c1ec84b
Sparse network support and nodepos read/write
2008-01-08 00:43:56 +00:00
bf29661af9
Added convertion to sparse format in category dataset
2008-01-07 13:13:27 +00:00
e6625c975f
bugfix
2008-01-07 12:44:08 +00:00
ca267920d8
Removed a couple of output datasets that did not work from pls.
2008-01-07 10:47:17 +00:00
bed280353b
Added support for sparse category-dataset
2008-01-06 17:01:00 +00:00
a84731da30
Support for icon assignment based on introspection
2007-12-17 18:52:49 +00:00
163271fc17
Correct behavior of dataset icons and names under transformations
2007-12-17 18:50:27 +00:00
083702b3b1
Fixed bug in color updating
2007-12-15 14:50:33 +00:00
e80440472d
Fixed axes scaling error in scatterplot
2007-12-14 17:27:12 +00:00
4de9a58ae9
Made a LoadDataFunction instead of four almost identical specialiced Funcions.
2007-12-14 16:45:05 +00:00
07477888bb
Fixed colormap bug
2007-12-14 15:43:35 +00:00
5c2df5c163
Removed get_project nonsense
2007-12-14 15:42:37 +00:00
6996aab2fa
Added log transform, support for multi selections in navigator-scatter, removed get_project-nonsense
2007-12-14 15:42:17 +00:00
a94c3ed1cc
Smoker workflow now loads data from correct path.
2007-12-14 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.
2007-12-14 11:48:21 +00:00
0e8d864ace
Does not need to import workflows.
2007-12-14 11:46:08 +00:00
7600abf372
Deleted all datasets. They don't belong here.
2007-12-12 17:02:28 +00:00
05cf63e694
Removes rpy, forcing scipy to be used.
2007-12-12 14:41:27 +00:00
455b2a7a86
Small fixes to setup.py and rules.
2007-12-11 19:49:36 +00:00
1798279a32
Files to debianize the program.
2007-12-11 18:26:47 +00:00
6379acca58
Added setup.py to do installation.
2007-12-11 18:25:08 +00:00
cef882b0a4
* Annotations are no longer cluttered as if they all belong to the same
...
dimension. There was a bug that actually gave the same annotation dictionary
to all dictionary annotation handlers.
* The selection window now remembers which annotation was shown for each
dimension.
2007-12-11 13:47:29 +00:00
c862c8bb04
Added function to specify a specific workflow based on module name.
2007-12-11 11:40:27 +00:00
9242b88d07
Removed buttons that do not belong on the toolbar: "New", "Load", "Save".
...
Load and save are currently not implemented anyway, but they do not represent
frequently used actions anyway.
2007-12-11 10:13:31 +00:00
90c84b768a
Changed help URLs.
2007-12-11 01:11:13 +00:00
057e2a9f1d
About to change the way logging is normally called.
2007-12-11 01:02:47 +00:00
d0a7b1cbc2
Code cleanup.
2007-12-11 00:13:26 +00:00
055c0ea4ac
Dataset dimensions are shown in statusbar.
2007-12-10 21:08:09 +00:00
1a4d73f26b
Fixed the function menu. It now works, is placed before "Help", and the method
...
for running a function is moved to the workflow module instead of being hidden the
WorkflowView.
2007-12-10 16:57:38 +00:00
82dacc3dd1
Added menu items to toggle visibility of workflow, navigator and infopane.
2007-12-06 00:20:42 +00:00
27d935319c
Added a delete function to the context menu on navigator elements.
2007-11-09 15:02:32 +00:00
c26999e688
Added line plot of matrices.
2007-11-08 11:47:36 +00:00
7ee7f0cf7e
Added scatter plotting from dataset in navigator.
2007-11-07 12:44:22 +00:00
aef2e1daf0
Tralala ...
2007-11-07 12:34:13 +00:00
ca51a0b382
Added mat2ftsv to naïvely convert matlab matrices to ftsv files. Works in at
...
least one case, but does not try to guess anything sensible for identifiers.
2007-10-31 17:43:02 +00:00
b114d5aeec
New crossval index generator
2007-09-25 06:31:40 +00:00
18f33decc7
Finnished the l-pls fdr
2007-09-21 13:16:40 +00:00
6698ebe932
Removed actiavtion in dimcontroller
...
opt. of compare func
2007-09-20 16:12:58 +00:00
41f93c5989
....
2007-09-20 16:11:37 +00:00
7e9a0882f1
Updates
2007-09-20 16:10:40 +00:00
d9e5398865
GO (id, description, definition, ontology)
2007-08-28 09:39:24 +00:00
16ed2fd9c9
u
2007-08-24 11:48:29 +00:00
dc43830752
HS-entrez annotations
2007-08-24 09:15:16 +00:00
7dbf28f65d
... just lots of stuff
2007-08-24 09:14:24 +00:00
21b63b17e5
Fixed axis bug in barplot
2007-08-24 09:13:34 +00:00
7538710144
Enabled tree lines and set sensitivity on transforms
2007-08-24 09:12:52 +00:00
fa4604dbe5
load dataset defaults to datadir
2007-08-22 14:05:51 +00:00
01ef4bdedd
Added support for identifiers sorting, and selection
2007-08-22 13:41:04 +00:00
ffe1ce6319
Fixed queries
2007-08-22 13:40:33 +00:00
6ba8c6eb67
ups
2007-08-21 10:31:09 +00:00
e06eeb6d17
ups
2007-08-21 10:25:23 +00:00
26ab6c3fe7
Added a "decimals" parameter to write_ftsv, so that datasets can be written
...
without full precision. Defaults to 7 digits after decimal point.
2007-08-16 10:02:54 +00:00
a6af506ae0
The reduced Uma X, for use in Lpls
2007-08-16 09:46:33 +00:00
fc91d17bdc
The Uma affy, nci60 + drug data + tissue type
2007-08-16 09:17:07 +00:00
d510e092e3
Added SAM and conditioned enrichment analysis
2007-08-14 16:16:31 +00:00
8d4848d5fa
Added explained variance
2007-08-14 16:12:28 +00:00
004cfe0a9f
Quick fix for gray on NaNs
2007-08-14 16:10:35 +00:00
13b35180ee
Fixed bug in DAG plot color mapping.
2007-08-08 12:24:14 +00:00
e08dba0924
read_ftsv and write_ftsv now supports filenames as well as file descriptors.
2007-08-08 12:23:45 +00:00
04126e9c83
New information content datasets.
2007-08-08 10:13:05 +00:00
46c2a0c149
New calculations (Z), based on updated X data
2007-08-07 11:45:16 +00:00
916fc4c046
Added scaling to navigator menu, moved transformations to a separate sub menu
2007-08-07 11:42:07 +00:00
168384f266
Cleaned esvd routine, added subfunc scale
2007-08-07 11:41:03 +00:00
d055a1f882
Some .....
2007-08-07 11:39:16 +00:00
4b80baf225
Added information content drag'n'drop to z loadings plot.
2007-08-06 16:20:39 +00:00
72e300c95e
Addded automatic bin selection in histogram plot
2007-08-04 10:37:22 +00:00
3f7215bc35
Factored out a mixin class for IC thresholding.
2007-08-03 12:09:17 +00:00
0523ebab05
Added dataset transpose option
2007-08-03 09:44:31 +00:00
e62a6ae9b3
Removed print statements
2007-08-02 14:51:53 +00:00
0758ab8bfb
Fixed histogram plot to accept selections of one, and made ad-hoc choice of proportional color to patches
2007-08-02 14:37:19 +00:00
7a0e2481eb
Full corrected X data
2007-08-02 11:22:05 +00:00
94f4b276b9
Fixed selection in DAG-plot to work both with and without IC set.
2007-08-02 11:20:30 +00:00
b334e94b15
New and corrected smokers data
2007-08-02 11:19:47 +00:00
438e7cb918
Irrelevant play
2007-08-02 11:19:16 +00:00
2d419a9862
Added GO-category enrichment analysis
2007-08-02 11:18:48 +00:00
973470b595
stuff
2007-08-02 11:18:18 +00:00
da5b977042
Moved less important datasets into a subfolder named "secondary".
2007-08-02 10:52:58 +00:00
83d76eac4f
Fixed vorrect namespace for scipy funcs
2007-08-02 10:44:06 +00:00
b233e4abc6
Added spin buttons for minimum and maximum information content in DAG plot.
2007-08-02 10:20:33 +00:00
dc3893eecc
Fixed a "main.project" bug
2007-08-02 10:19:16 +00:00
f12fe23c1b
Fixed docstrings.
2007-08-02 10:08:52 +00:00
4c24061575
Fixed docstrings.
2007-08-02 10:08:27 +00:00
63d6347f37
Fixed makefile to not use lots of space on inherited function documentation.
2007-08-02 10:04:06 +00:00
6e4db7ebe4
Fixed plot focus signal problem.
2007-07-31 12:25:56 +00:00
10eba079bc
iii
2007-07-30 18:04:42 +00:00
aa4007e208
Improved drag'n'drop of data into scatter plots so that it no longer requires
...
matching identifiers along dimensions.
2007-07-30 17:42:48 +00:00
0bc4a6e3f0
Fixed drag'n'drop of datasets to DAG-plots to convert inf/-inf to
...
maximum/minimum values of the dataset.
2007-07-30 14:15:23 +00:00
e84a202fbe
Commented out unused functions.
2007-07-30 10:51:58 +00:00
50a6dae3f6
added full lpls data
2007-07-30 10:21:09 +00:00
b39e71ca2b
Trying to fix cv_pls
2007-07-30 09:46:43 +00:00
9ccdf97d07
Changed filenames of information content datasets.
2007-07-30 07:55:36 +00:00
1e18ac81de
Added names to datasets.
2007-07-30 07:54:22 +00:00
349cab3c51
ups
2007-07-28 16:05:11 +00:00
9a2e259209
c
2007-07-28 09:19:42 +00:00
df88f44255
clean up
...
ups
2007-07-28 09:18:48 +00:00
5cf34fc03f
Added information content datasets.
...
They are in files named ICs<subgraph><number> where
those numbered 0 uses all ECs while 5 uses only the safest ones.
2007-07-27 17:22:10 +00:00
4b8f594966
app -> main.application
2007-07-27 09:40:58 +00:00
47b89cc411
Fixed bug in esvd for m>n
2007-07-26 18:32:48 +00:00
7fd4ac6225
pls opt fix
2007-07-26 18:32:27 +00:00
b35f814ef0
Added center check button on lineview
2007-07-26 18:26:50 +00:00
dc7f7dbde2
Added existing_identifiers function to Dataset.
...
Added colouring drag'n'drop to DAGPlot in gobrowser module.
2007-07-26 15:45:42 +00:00
a45743c31e
Added main.py that now contains the One & Only Singleton instance of these classes:
...
- Navigator
- Aplication
- Workflow
- Project
- Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.
2007-07-26 12:35:59 +00:00
91abf12f51
sd
2007-07-24 14:34:47 +00:00
13dc6de5c1
Name annotations to go-terms.
2007-07-24 13:34:40 +00:00
1d517d0754
Changed hardcoded absolute path to relative path.
2007-07-24 13:00:29 +00:00
524c90fcf7
Updated to handle new numpy/scipy.
2007-07-24 12:19:13 +00:00
05274b4f0b
confidence
2007-07-23 18:07:10 +00:00
939dba20ee
first import lpls
2007-07-23 17:35:28 +00:00
54d271b841
go test data
2007-07-23 17:35:04 +00:00
a05d0faa0d
Lib updates
2007-07-23 17:33:21 +00:00
7ea87e646a
Added DAG plot to gobrowser module and smokers workflow.
2007-07-23 17:02:28 +00:00
155dfada5c
iups
2007-07-23 13:25:34 +00:00
9db5991108
2007-07-20 15:48:59 +00:00
98f53d3448
updates
2007-07-20 12:32:54 +00:00
7ee7aa968a
Initial import
2007-07-20 09:36:26 +00:00
dd04e28a62
Query fix
2007-07-05 18:49:24 +00:00
850deeec0d
Renamed gene identifers to gene_id
2007-07-05 18:40:29 +00:00
75c7c51708
DistanceToSelectionFunction
2007-07-05 18:36:59 +00:00
3f5d45d7af
Renamed smalltest workflow to smokers.
2007-07-05 18:24:45 +00:00
fae096afe4
Changed workflow name from smalltest to smokers, because it is heavily based
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on the smokers dataset.
2007-07-05 13:20:52 +00:00
a503ffcdf8
Fixed linewidth in selection in scatter plots.
2007-07-05 11:57:21 +00:00
d29013a863
T-test now works, and outputs a histogram as well as t-values and p-values.
2007-07-03 16:25:38 +00:00
99987999db
Broke up a too long line.
2007-07-02 09:54:56 +00:00
884804c49a
Added a dummy for the t-test function. Will be updated when I have access to my
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office computer tomorrow.
2007-06-28 21:48:13 +00:00
b637a5badc
Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have
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trouble running the app.
2007-06-28 21:42:18 +00:00
4eaea2fe59
Added empty lists as default values for all_data and all_plots in Options, so
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that subclasses of Options will work with the GUI without modifications.
2007-06-28 21:33:09 +00:00
7b20f44fef
Added a GO similarity function that does not do anything useful yet.
2007-06-22 15:37:59 +00:00
e5cd8a8077
Started on a function to enhance gene lists by using GO similarities.
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Not in a usable state.
2007-06-22 15:37:22 +00:00
68cc583d2c
Added common_dimensions(ds) that lists common dimensions between two
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datasets.
2007-06-22 15:35:45 +00:00
ff8833a22c
Added read functions for the medium and large smokers sets.
2007-06-21 10:28:10 +00:00
d6298a2d99
Ensures that the GO is only loaded once.
2007-06-21 10:26:35 +00:00
ff2c42902f
Commented out some log lines that just cluttered the log.
2007-06-21 10:25:17 +00:00
2eb3d71a5d
Moved data/smokers-med to data/smokers-medium.
2007-05-16 15:35:25 +00:00
91032d729e
Some more smoker data
2007-05-16 11:45:43 +00:00
7bdfdea23b
Added -d option to get all identifiers along a single dimension.
2007-05-16 10:30:54 +00:00
c7bfefe358
Fixed resnik distances.
2007-05-15 18:16:07 +00:00
335efe231a
go-gene-matrix takes a GO vs. GO distance matrix and a gene-go-mapping file
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and makes a gene vs. go distance matrix based on the shortest distances found
between each gene and go term.
2007-05-15 18:15:51 +00:00
1ab558248c
Piping information through dataset -i works. Added names of planned features
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to the dataset script.
2007-05-09 21:52:59 +00:00
7272eb63d2
Working on a script to query datasets without starting fluents.
2007-05-09 17:41:50 +00:00
ebe7621817
some biocondoctur utilities
2007-05-06 13:51:06 +00:00
f1301be67a
go-distance update.
2007-04-26 18:54:34 +00:00
a0faed2614
Forgot some ...
2007-04-24 17:21:40 +00:00
34ae426c86
Added correlation plot and moved colorbar to plots
2007-04-24 17:17:31 +00:00
90bb25eb55
added default mappable to None
2007-04-24 17:16:34 +00:00
31ac569c3e
Added colorbar shortcut
2007-04-24 17:04:29 +00:00
fefaffb2e3
go-distance seems to be able to calculate resnik now. Not asserted with
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calculations by hand.
2007-04-04 19:08:50 +00:00
28f0f53e8a
go-distance script soon calculating resnik distances.
2007-04-03 13:08:48 +00:00
a5c3a1f154
A couple of extra lines of code in a script.
2007-03-27 13:02:22 +00:00
728c334e8a
ontology distance script now accumulates annotations correctly.
2007-03-26 23:15:14 +00:00
11eb3306b9
Works a bit better.
2007-03-26 17:18:26 +00:00
947cf8385f
Annotations on yeast from Stanford mdb.
2007-03-23 20:51:04 +00:00
0904a59310
Gene ontolgy distance script in C. Will hopefully speed up calculations when
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finished.
2007-03-23 13:25:07 +00:00
6f19fe1b4b
Resnick distance matrix
2007-03-16 17:05:46 +00:00
0eff457910
Added biological process info to the small smokers example, and a README file to
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explain the dataset, at least the non-trivial parts.
2007-03-15 23:57:35 +00:00
3dc1867be4
Added entrez-go-mapping that maps entrez IDs to GO terms based on a file of the form:
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affy_id ::: geneid_1 /// geneid_2 ::: go(bp) ::: go(cc) ::: go(mf)
2007-03-15 23:47:24 +00:00
6fe4ff3c59
Added scripts folder for small but useful scripts.
2007-03-15 12:46:41 +00:00
b02773b4e6
pls loading plot now have correct name
2007-03-15 10:38:52 +00:00
dbe49b366d
added import of networkx
2007-03-15 10:38:05 +00:00
f6696dfacc
Added gobrowser to smalltest workflow.
2007-03-14 21:08:56 +00:00
1c48315a0f
Added debug output.
2007-03-14 17:26:40 +00:00
438a268b1d
Inserted visible header sort
2007-03-14 16:34:50 +00:00
3d2492578e
whitespace
2007-03-14 16:33:54 +00:00
3bd21ab089
metric support
2007-03-14 16:33:16 +00:00
48047f1395
Moved lots of stuff back to sandbox
2007-03-14 16:32:49 +00:00
7f1f639ee7
Updates on metric, whitespace
2007-03-14 16:31:25 +00:00
22f6e3284c
whitespace
2007-03-14 16:30:18 +00:00
818dc0b2b0
added a logger for constructor calls
2007-03-14 16:27:23 +00:00
212da78933
correct comp update
2007-03-14 16:17:21 +00:00
00dd3e8d9d
added validation on identifiers input
2007-03-14 16:06:16 +00:00
51435d9fdc
Fixed dataset type to network
2007-03-14 10:27:08 +00:00
ac447546a2
Annotation file for dim: gene_id
2007-03-14 10:26:11 +00:00
a9981779a6
network of articles
2007-03-14 10:25:35 +00:00
9cbefb5705
in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations
2007-03-14 10:24:49 +00:00
6cbf6d0689
Initial commit of small example test workflow
2007-03-13 15:24:20 +00:00
6b2737efb9
Added a line.
2007-03-09 14:33:09 +00:00
f61bc353a9
Typofix
2007-03-09 14:30:40 +00:00
5be2f1faf6
Initial import of Iris data
2007-03-04 21:00:39 +00:00
ae9a207a71
Added a tag column in the GO browser to help link it to selections.
2007-03-01 19:13:13 +00:00
442b5fed5f
Moved all files to the smokers-small subdirectory.
2007-03-01 19:12:40 +00:00
f31795ac2a
Corrected erroneous checkin.
2007-03-01 15:27:50 +00:00
e01dd578cd
Preserves PYTHONPATH
2007-03-01 15:27:24 +00:00
ff070e5312
Preserves PYTHONPATH.
2007-03-01 15:26:38 +00:00
28e6c52f78
Fixed bug with hidden dimensions.
2007-03-01 15:06:33 +00:00
d699afa6a5
fixed bu when trying to drag anything over an empty view
2007-03-01 15:03:53 +00:00
f8f3bd712e
Smoker example data
2007-03-01 15:01:30 +00:00
6101bf850c
Changed CategoryDataset ftsv files to be written with 0 and 1 instead of True and False.
2007-02-28 16:33:11 +00:00
89636962a7
Added Workflow.get_data_file_name() which returns the full path to a given
...
data file, or None if the file does not exist. This is tested in the test
workflow.
2007-02-28 14:56:24 +00:00
934640ea62
Searches for /etc/fluentsrc and ~/.fluents configuration files. Adds the
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home configuration variable.
2007-02-28 14:07:33 +00:00
281337251d
Added selection of lines in network plot
2007-02-27 21:19:24 +00:00
78183df0e9
Alignment of function boxes
2007-02-27 18:14:58 +00:00
b754a5df44
Update from change of plots/view
2007-02-27 16:31:18 +00:00
61cfd00558
Division of plots -> view/plots
2007-02-27 16:28:03 +00:00
059cddbc16
Division of plots -> view/plots
2007-02-27 16:27:39 +00:00
bf1ad1be87
Removed old help function.
2007-02-27 16:25:48 +00:00
1ba4bf5f82
Initial config parser support.
2007-02-27 16:08:22 +00:00
686a1fdcd1
network/venn plot now maximizes the space available
2007-02-27 15:42:27 +00:00
d27278241c
oops ... (broken code fixed)
2007-02-27 15:08:00 +00:00
4de65f1085
Clean up
2007-02-27 15:05:21 +00:00
f73a6db0ee
Added ctrl+arrows to navigate between plots.
2007-02-26 23:00:25 +00:00
eacb44f32a
Removed "Edit" menu.
2007-02-26 22:12:32 +00:00
d040f11c2f
Added identifier list update on selection changed.
2007-02-26 18:02:34 +00:00
537dc9f0ec
Cleanup of selection browser module. Added comments, fixed some bits of code.
2007-02-26 14:35:31 +00:00
c0bbe24c39
No selections in scatter marker now updates to no selection instead of last selection
2007-02-26 12:11:28 +00:00
a6fbef9cfa
scatter plot selected markers are now on top (visible)
2007-02-26 11:20:02 +00:00
2f60d0663d
Clean up of import statements
2007-02-26 09:08:50 +00:00
5ed602f355
Lots of changes .... (new selector, mode updates, histogram selection, ++)
2007-02-26 08:00:36 +00:00
3ee8439e07
Added selection listeners to plots in context menu
2007-02-26 07:58:33 +00:00
a614908436
Size of current selection is now updated in details
2007-02-23 11:12:03 +00:00
41e8ed511b
Fixed dim_cursor_changed to to use the correct treemodel, and added show/hide on selection details
2007-02-23 10:46:04 +00:00
0d8702bb71
added show/hide on dimensions
2007-02-21 19:57:27 +00:00
2bae169f38
Annotation display now works (sort of).
2007-02-21 16:39:04 +00:00
28aca8c621
added project to selection controller
2007-02-21 13:57:48 +00:00
8c03338b75
hypergeometric test (scipy version has errors)
2007-02-21 13:03:51 +00:00
48165d1aed
Updated the selection controller with sorting ++
2007-02-21 12:41:37 +00:00
f0b2660813
Selection listeners are now notified when new dimensions are added (because
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this implies that an empty selection is made on the new dimension).
2007-02-21 12:05:08 +00:00
5800e7e362
Fixed a bug that prevented the first selection on a dimension to come from a
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dataset.
2007-02-21 11:49:43 +00:00
a5955f9b59
Now updates the DimListConroller when a CategoryDataset is drag'n'dropped into
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SelectionListController.
2007-02-21 11:43:00 +00:00
c5c4f13a19
Fixed some excessively long lines.
2007-02-21 11:08:20 +00:00
2cc4e86b0a
Split selections.py into three different controller classes, one for each list. There
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is still some work to be done, and bugs to be fixed.
2007-02-21 00:00:26 +00:00
a2195bcb4b
Added Import annotations option.
2007-02-16 11:23:29 +00:00
93a2f404d2
Data needed if annotationtest should run clean.
2007-02-15 23:09:49 +00:00
6809c1a454
Added some annotation support in selections.py, including the beginning of a
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menu option to add an arbitrary annotation alongside identifiers.
2007-02-15 22:57:40 +00:00
953662e1fb
Added a couple of more assertions to the test of read_annotations_file()
2007-02-15 22:54:08 +00:00
e6cf8f765a
Added read_annotations_file()
2007-02-15 22:49:40 +00:00
b17f04466b
Added read_annotations_file() which reads a tab delimited file containing
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annotations to identifiers along a dimension.
2007-02-15 22:42:55 +00:00
4319e8630e
fixed error in typechecking
2007-02-15 13:36:36 +00:00
fc33c2dbfc
factored out packer
2007-02-09 14:02:58 +00:00
15c89fb9b5
Factored out packer
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A packer.py
2007-02-09 14:02:39 +00:00
7eb13b14cb
Removed resolution arg to Circle to avoid construction of a circlepolygon (deprecated)
2007-02-02 12:21:19 +00:00
320cd97512
Removed noise generating print statements.
2007-01-31 14:58:37 +00:00
75b66914fd
Fixed bug by removing hardcoded filename.
2007-01-31 14:56:43 +00:00
74cb30428c
Added annotations to identifiers, and converted the unused annotationtest.py to
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test the new module.
2007-01-31 14:19:23 +00:00
1863bfc564
Save plot enabled
2007-01-31 13:26:46 +00:00
a7c60ffe64
added venn diagram test plot
2007-01-31 13:03:27 +00:00
240b0a4a9f
New lasso icon
2007-01-31 13:02:25 +00:00
d1205ae67f
Removed colorbar
2007-01-31 13:01:09 +00:00
37feb1c25b
bugfix on P scale
2007-01-31 13:00:36 +00:00
2cfa3ca415
spin on a/o, colorbar on keypress
2007-01-31 12:59:21 +00:00
63be80aa92
pls options added
2007-01-31 12:03:11 +00:00
088f180b5d
Barplot, lots of changes in scatter, disabled modes, removed labels, bugfix on lasso
2007-01-31 12:02:11 +00:00
e716db3fd2
Added center option to validation, + naming updates
2007-01-31 11:59:23 +00:00
29509902df
bugfix on shape
2007-01-31 11:57:59 +00:00
8e607c7b1a
bugfixed scaling issues
2007-01-31 11:57:04 +00:00
f064b7134d
Removed scale option added pack
2007-01-31 11:56:28 +00:00
1d5929f14c
pls options glade file
2007-01-31 11:55:43 +00:00
ed2848beb3
Errors when identifers dont match shape, + whitespace
2007-01-31 11:54:54 +00:00
48bb47ec86
Bugfixed pca
2007-01-25 12:36:32 +00:00
aeb37cf4cd
Added supportp for tall X in PCA
2007-01-25 12:17:16 +00:00
fa3722600c
pca options glade file
2007-01-25 12:15:30 +00:00
61bfc236e6
Changed location of PCA options glade file.
2007-01-25 12:15:19 +00:00
7a204a3426
Added option page to option dialog
2007-01-25 12:10:18 +00:00
1c2c2c8895
Multiple lib changes
2007-01-25 11:58:10 +00:00
a65d79697f
Added Expand/Collapse menu choices to the GO browser context menu. This is
...
particularly useful when searching for GO terms, because the gtk TreeView
widget does not do interactive search in collapsed parts of the tree.
2007-01-21 16:16:37 +00:00
e03cc4ed4c
Added a ScrolledWindow around the navigator.
2007-01-19 14:00:10 +00:00
7693f336ba
Added a singleton project in the project module, so that the current project is
...
easily accessible from anywhere in the code. As there is only one project at
any given time this should not be a problem.
The Gene Ontology browser needed this to be able to set the selection without
passing the current project through several constructors.
Added a context menu in the GO browser that allows the user to select all GO
terms in the subgraph that starts on the current node.
2007-01-18 15:45:48 +00:00
f533344242
Added histogram in plot menu
2007-01-17 15:40:54 +00:00
7c20e6d780
Added simple histogram
2007-01-17 15:40:33 +00:00
1ffbf4f9e7
Added default implementation of set_current_selection in Plot, so that plots can safely
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ignore selections without adding any code to the plot.
Rectangle select mode, lasso select mode and freeze are now grayed out in ImagePlot.
2007-01-17 15:35:12 +00:00
06591e301e
Added "Plot" submenu in navigator context menu. Can create an ImagePlot of a dataset.
2007-01-17 14:06:07 +00:00
c3c6e85044
Added ImagePlot, which displays a dataset as an image.
2007-01-17 13:20:04 +00:00
33c51505c4
Fixed the dataset loading so that it returns a correctly named Dataset.
2007-01-16 12:41:29 +00:00
f612dda72f
Fixed bug in ftsv save and open dialogs. The save dialog now looks as intended.
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Added the possibility to load several datasets at once. Error handling should still
be improved.
2007-01-16 12:28:56 +00:00
ea4c0af6de
fixed shift/control on lasso
2007-01-15 15:46:24 +00:00
cacb0a27b7
Added "Save dataset" option to navigator context menu.
2007-01-15 13:58:56 +00:00
