genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2017-05-16	Fixed issue that caused mapping to not work for R/qtl	zsloan
	Updated dataset menu dropdown info Began adding option to download statistics figures as PNG
2017-04-25	Fixed issue with correlation result trait links if target dataset is ↵	zsloan
	different from base dataset Improved collection list and view table appearances Added question mark image for glossary entries in table headers Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values
2017-04-17	Added option to remove collections from collection list page	zsloan
	Improved appearance of search result and collection tables
2017-04-05	Added images directory with various gifs, etc	zsloan

2017-04-05	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into development	zsloan

2017-04-05	- Temporary traits can be created, viewed, and added to collections	zsloan
	- Correct PCA trait data is created but can't be saved yet - Added inner margins by increasing xDomain and yDomain of probability plot on trait page - Increased X/Y-axis label font size - Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading - Improved appearance of correlation page table - Added links to github to index page - Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those - Removed "Tissue" from trait page for phenotype traits
2017-04-04	Change scatterplot image buffer/inner	Lei Yan

2017-04-04	align X and Y meta info	Lei Yan

2017-03-30	Change "Correlation Scatterplot" size, font, color, etc.	Lei Yan

2017-03-16	Merge /home/zas1024/gene	Lei Yan

2017-03-16	Add meta info (X axis, Y axis) for Correlation Scatterplot	Lei Yan

2017-02-09	Fixed issue where I forgot to add GeneticType to the query_for_group query ↵	zsloan
	for non-mRNA Assay datasets Increased digits of some Basic Statistics values from 2 to 3
2017-02-09	Changed second column header to 'Value' when there's only one sample group	zsloan

2017-02-09	Added genetic_type to DatasetGroup object to differentiate between which ↵	zsloan
	groups should show dominance effect Minor changes/improvements for trait page Updated dataset_menu_structure.json
2017-02-08	Changed the way .fam files are written/read, which fixes the issue with ↵	zsloan
	GEMMA mapping accuracy.
2017-02-06	Mapping results figure now correctly says whether GEMMA was used as mapping ↵	zsloan
	method.
2017-02-06	Merge branch 'development' of github.com:zsloan/genenetwork2	zsloan

2017-02-06	Commented out reference to trait_submission since it's not used yet	zsloan

2017-02-06	Merge branch 'master' of github.com:zsloan/genenetwork2	zsloan

2017-02-06	Fixed appearance of several tables (search, mapping results, sample data)	zsloan
	Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
2017-02-02	Merge /home/zas1024/gene	Lei Yan

2017-01-26	Merge pull request #1 from genenetwork/testing	zsloan
	Various changes/fixes
2017-01-26	GEMMA now works with CFW data (had to update where it looks for the input ↵	zsloan
	files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
2017-01-03	Fixed appearance of samples tables in show_trait to look like all the other ↵	zsloan
	tables Disabled sorting for the first column (check box) of the samples tables
2016-12-15	Merge pull request #234 from zsloan/master	zsloan
	Various changes
2016-12-15	Changed table appearance	zsloan
	Updated dataset_menu_structure.json
2016-12-13	Fixed a problem related to the last commit that caused a problem when ↵	zsloan
	loading a collection or doing ctl analysis
2016-12-12	Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵	zsloan
	be there and changed the code that calls them accordingly Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json
2016-11-29	Fixed loadings plot so it looks like the GN1 figure	zsloan

2016-11-21	Fixed correlation page so it correctly sorts by the scientific notation for ↵	zsloan
	sample p Set default sort for correlation page to sample p Improved appearance of correlation matrix some by decreasing line height Added labels to each figure/table on the correlation page
2016-11-18	Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) ↵	Lei Yan
	(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
2016-11-15	Fixed issue where sample values of 0 would sometimes be displayed as 'x', ↵	zsloan
	which would result in wrong correlation results Fixed issue where the mean would sometimes be displayed into of the additive effect
2016-11-11	Fixed error causing correlation matrix page to not work with 2 traits ↵	zsloan
	(related to factor loadings table) Also improved factor loads table to show only two factors when there are two traits Fixed error related to get_traits_from_collections.js being called in collections/list before jquery is defined
2016-11-11	Fixed problem that caused checkboxes to not work with Scroller search ↵	zsloan
	results pages Improved the way the table width is set for search results page
2016-11-08	Adding the joss badge	DannyArends

2016-11-07	Adding functions addNode and addEdge, to separate out the cytoscape graph ↵	DannyArends
	creation from the main CTL analysis code
2016-11-07	Adding the reference to the paper, and updating the output to show the ↵	DannyArends
	cytoscape.js network
2016-11-07	Adding code to the ctl analysis file to output nodes and edges for cytoscape	DannyArends

2016-11-07	Javascript file (based on the correlation file) to dsplay CTL networks using ↵	DannyArends
	cytoscape.js
2016-11-02	Fixed typos causing genofile selector to not show up in mapping options	zsloan

2016-11-02	Added toggleable short and long labels to correlation matrix	zsloan
	Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
2016-11-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-11-02	Added Scroller functionality to regular (but not global) search, which ↵	zsloan
	increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
2016-10-31	Merge branch 'lyan' into testing	Pjotr Prins

2016-10-31	Use existing GENODIR - the metadata can be stored there, next to the	Pjotr Prins
	.geno files.
2016-10-31	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	Pjotr Prins

2016-10-31	Fix spacing	Pjotr Prins

2016-10-31	Merge branch 'master' of github.com:lyan6/genenetwork2 into lyan	Pjotr Prins

2016-10-29	For those case that we have multiple genotypes we would like to add a selector.	Lei Yan

2016-10-25	Just removed some extraneous spaces in trait.py	zsloan