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2017-02-09Added 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
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
2017-02-06Mapping results figure now correctly says whether GEMMA was used as mapping ↵zsloan
method.
2017-02-06Merge branch 'development' of github.com:zsloan/genenetwork2zsloan
2017-02-06Commented out reference to trait_submission since it's not used yetzsloan
2017-02-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2017-02-06Fixed 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
2017-01-26Merge pull request #1 from genenetwork/testingzsloan
Various changes/fixes
2017-01-26GEMMA 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
2017-01-03Fixed 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
2016-12-15Merge pull request #234 from zsloan/masterzsloan
Various changes
2016-12-15Changed table appearancezsloan
Updated dataset_menu_structure.json
2016-12-13Fixed a problem related to the last commit that caused a problem when ↵zsloan
loading a collection or doing ctl analysis
2016-12-12Moved 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
2016-11-29Fixed loadings plot so it looks like the GN1 figurezsloan
2016-11-21Fixed 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
2016-11-21Merge pull request #235 from lyan6/masterPjotr Prins
Thanks. Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalErro…
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) ↵Lei Yan
(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
2016-11-15Fixed 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
2016-11-11Fixed 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
2016-11-11Fixed 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
2016-11-08READMEPjotr Prins
2016-11-08Merge pull request #232 from DannyArends/testingPjotr Prins
Updates to the CTL analysis
2016-11-08Adding the joss badgeDannyArends
2016-11-08Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingDannyArends
2016-11-07Adding functions addNode and addEdge, to separate out the cytoscape graph ↵DannyArends
creation from the main CTL analysis code
2016-11-07Adding the reference to the paper, and updating the output to show the ↵DannyArends
cytoscape.js network
2016-11-07Adding code to the ctl analysis file to output nodes and edges for cytoscapeDannyArends
2016-11-07Javascript file (based on the correlation file) to dsplay CTL networks using ↵DannyArends
cytoscape.js
2016-11-03Updated to use gn-deployPjotr Prins
2016-11-02Fixed typos causing genofile selector to not show up in mapping optionszsloan
2016-11-02Added toggleable short and long labels to correlation matrixzsloan
Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
2016-11-02Fixing docsPjotr Prins
2016-11-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-11-02Added 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
2016-10-31Merge branch 'lyan' into testingPjotr Prins
2016-10-31Use existing GENODIR - the metadata can be stored there, next to thePjotr Prins
.geno files.
2016-10-31Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingPjotr Prins
2016-10-31Fix spacingPjotr Prins
2016-10-31Merge branch 'master' of github.com:lyan6/genenetwork2 into lyanPjotr Prins
2016-10-29For those case that we have multiple genotypes we would like to add a selector.Lei Yan
2016-10-25Merge pull request #216 from zsloan/masterPjotr Prins
Replaced Download Table in view_collection page with python version
2016-10-25Just removed some extraneous spaces in trait.pyzsloan
2016-10-25Replaced the Download Table button for collection page with python version ↵zsloan
that displays metadata, etc Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
2016-10-24Merge pull request #214 from zsloan/masterPjotr Prins
Thanks! Download table rewritten in Python to add extra functionality
2016-10-21Added CSV table download option to both gene and pheno global searchzsloan
The "Database" part of the metadata isn't displayed for global search table downloads In both regular and global search, the table can not be sorted by whether the first column is checked Removed some unused datatables/javascript from the regular and global search page html
2016-10-21Added metadata to "Download Table"zsloan
Only checked traits are now downloaded and all traits are downloaded if nothing is checked
2016-10-19Rewrote export CSV in pythonzsloan
Still need to add metadata and change it to where only selected traits are exported
2016-10-18Merge pull request #213 from zsloan/developmentPjotr Prins
Fixed issue where period sometimes appeared incorrectly in search res…
2016-10-17Fixed issue where period sometimes appeared incorrectly in search results text.zsloan
Changed formatting of a couple things in search results text (capitalizing/underlining "terms" and bolding the search term) Changed "Gene" label on trait page to "NCBI" and removed GenBank link
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