Commit Graph

64 Commits

Author SHA1 Message Date
c40f9a2947 Added a LineViewPlot in GenerateData 2006-10-17 13:59:31 +00:00
e0ca48d4b3 Changed how the selection list works. CategoryDatasets can be dragged down to
the selection list, and will then be converted to Selections.
2006-09-08 18:25:03 +00:00
f47a9066e3 Removed print statements. 2006-08-31 12:24:06 +00:00
0b58c5ea28 Switch to numpy (scipy_version>1.0) changes 2006-08-31 10:04:19 +00:00
a0786d521a Removed SinePlot from the test workflow. 2006-08-30 14:38:33 +00:00
1b9aff1c5a The selection view now works. Functions can return a dataset.Selection object which will be stored in the selection list. 2006-08-29 23:57:21 +00:00
97e652edce fixes 2006-08-28 12:06:05 +00:00
fc8b2e601f update 2006-08-14 11:52:26 +00:00
b769288b3b Added a selection view tab, placed next to the "Log" tab. The tab currently
only displays the current selection.
2006-08-07 14:14:42 +00:00
4c716e9428 NetworkPlot now works, but does not allow node colors or sizes to be passed as keyword arguments. 2006-08-03 14:30:06 +00:00
b3d681ef16 * system/plots.py: Added NetworkPlot, which may or may not work correctly.
* system/dataset.py: Removed a few lines of obsolete code.
2006-08-01 13:22:39 +00:00
87f87e36c8 * system/fluents.py: Fixed a bug where the the application tried to load
a toolbar from None

 * system/plots.py: Fixed MainView.insert_view that was a no-op when in large
   view.

 * system/dataset.py: Changed __str__ of dataset to also show names of dimensions.
2006-07-21 14:30:09 +00:00
9ab1ebe687 Small cleanup. 2006-05-09 14:16:22 +00:00
443b18cea6 Made sure ordering of matrices are ok. 2006-05-09 14:13:09 +00:00
86f89b6ffe Typo. 2006-05-09 13:51:14 +00:00
5b1af849dc Implemented Limma function for Affy workflow.
Extended ScatterPlot to take two datasets and updated code using it.
2006-05-09 13:17:17 +00:00
0db25f1dd7 Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it. 2006-05-05 14:43:53 +00:00
97f56f66ac Added text-input for contrast-matrix creator for affymetrics workflow. 2006-05-05 14:30:23 +00:00
aa3a9ab619 Added automagic argument checking when running functions. 2006-05-05 10:10:03 +00:00
fafa373e67 Added categorygetter for PhenotypeDataset. 2006-05-04 13:30:04 +00:00
fb7128138e Fixed floats in phenotype importer.
Added PrintFunction for debug-printing.
Added PhenotypeImportFunction to AffyWorkflow.
2006-05-03 14:27:38 +00:00
b757da5929 Implemented PhenotypeDataset with tests. 2006-05-03 14:04:28 +00:00
56a6028547 Validation on number of inputs added 2006-05-03 11:52:54 +00:00
5b2223afcd Multiselection included. (Without input validation). 2006-05-03 11:11:45 +00:00
a2d3a9d5cc Made PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input. 2006-04-28 11:44:55 +00:00
8fd1f4ba83 Renamed module for affy workflow. 2006-04-27 15:06:01 +00:00
0df56248ee Removed obsolete module annotations. 2006-04-27 12:41:51 +00:00
fe0cf736f5 Created affy workflow. 2006-04-27 12:15:30 +00:00
3683f6c2e9 Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot. 2006-04-27 11:38:40 +00:00
969006015a Added LinePlot used by Affy importer. 2006-04-27 11:03:11 +00:00
251f9d6cf4 Added command line options to create a new project based on a given workflow. 2006-04-25 12:19:25 +00:00
359903c5ab Made system a package. 2006-04-25 09:53:35 +00:00
cfbb76f25a import * removed 2006-04-24 16:05:54 +00:00
ba2a769f01 Function names are now folders in the navigator. 2006-04-24 15:20:27 +00:00
179a2f88a9 The navigator now displays the plots and data in a tree that shows the ancestry information. 2006-04-24 14:52:21 +00:00
6c72dec7fa Removed need to provide plots with project/workflow on creation, is instead injected by project itself when added to it. 2006-04-24 14:42:45 +00:00
97e09b39a1 Added matrix-getter to Dataset.
Added rma-function to preprocessing incorporated in AffyMatrix-importer.
Added PCAFunction to go_workflow for processing loaded affymatrix data.
2006-04-24 14:07:34 +00:00
cebf801cf6 bugix on creation of output data (E) from pca 2006-04-24 12:51:43 +00:00
6356e2ebd6 get_dim_names and get_identifiers added in dataset 2006-04-24 11:23:30 +00:00
a2e4392a72 Complete rewrite of dataset class, with (all) the necessary updates 2006-04-24 09:53:07 +00:00
e762aef882 * system/dialogs.py: Oooops. Forgot this file in the previous commits. Well,
here it is, currently only with the New Project dialog.
2006-04-22 22:29:02 +00:00
f484ec9945 * workflows/go_workflow.py: Added a workflow name to make it identifiable
in the "create project" druid.
2006-04-22 21:48:30 +00:00
efcdafe843 * The New project toolbar button now works. A druid will display the
available workflows and ask you to select one of them. There are still
   a couple of unresolved issues, but it works, so i upload it to ease
   the use of the program.
2006-04-22 21:46:44 +00:00
357cd1a1a6 Removed workflow being dependent on rpy by putting the import within the run function of affymatrix import. 2006-04-22 20:48:44 +00:00
26f16acc9c Made sure pickling use protocol 2 to make it faster and the files smaller (binary). 2006-04-22 18:11:31 +00:00
553bfbe1ae Big cleanup of affymatrix importer. Now use E@exprs to get matrix from loaded data.
Also made row and colname import better by ensuring vector-handling, ensuring that getting single column/row data works without being converted into a single string instead of string in a list.
Removed ;1-hack and use NO_CONVERSION to ensure no extra computation is done when calculating r stuff.
Now AffyMatrix data is named as such.
2006-04-22 17:59:15 +00:00
5a2a1afe91 Added pickling as a quick and dirty way of loading and saving data in einars workflow. 2006-04-22 16:27:33 +00:00
d123f0e1c1 Added doc-string for CelFileImportFunction. 2006-04-22 15:59:19 +00:00
23914b2d1e Added support for affy cel files. 2006-04-22 00:17:22 +00:00
c601ad3966 Removed data information as function in workflow and added as default action on datasets double-clicked in navigator. 2006-04-21 15:02:13 +00:00