aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2016-04-29Fixed database link in trait page detailszsloan
2016-04-29Also fixed links in statistics section (for normal probability plot) and ↵zsloan
removed 'target=_blank's
2016-04-29Fixed links in correlation descriptions on trait page and removed ↵zsloan
target=_blank (so will not open in new window unless user specifies) Fixed javascript so description changes when user changes the method and "Type" option is removed for literature correlation
2016-04-28Added option to export permutation results for mapping pagezsloan
Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border
2016-04-25Interval Analyst table mostly working, just need to work out a few more thingszsloan
2016-04-22Fixed issue where manhattan plot setting wasn't being carried over to single ↵zsloan
chromosome view for mapping results Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
2016-04-20Interval Mapping now correctly does interval mapping if Marker Regression ↵zsloan
isn't checked (it used to just "connect the dots" of the marker regression output) Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
2016-04-20Added borders to stats table in trait pagezsloan
2016-04-18Additive effect lines are now separated by chromosome (like the qtl line in ↵zsloan
the last commit) Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later
2016-04-14Fixed issue where qtl lines in interval mapping wouldn't connect between ↵zsloan
chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-04-07Added option to change the maximum y-axis value for GN1 mapping figurezsloan
2016-04-07Permutation figure and x-axis label should change to correctly reflect the ↵zsloan
mapping scale (lrs or lod) Fixed bug where broken image link would appear if you ran R/qtl with no permutations
2016-04-07SNP Track option should now work for GN1 mapping figurezsloan
Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06The option to switch between LRS and LOD for the GN1 mapping figure should ↵zsloan
now work correctly. The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
2016-04-06Setting lodm to always be 1.0 fixes the issue where it would incorrectly ↵zsloan
display LOD scores for the Y-Axis instead of LRS values
2016-04-06Permutations (suggestive/significant lines, legend, and histogram) should ↵zsloan
now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2016-04-05Bootstrap test should now work correctly for qtl reaper mapping method on ↵zsloan
full genome view There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
2016-04-05Fixed issue where haplotype analyst option would appear when using ↵zsloan
genetic(centimorgan) mapping
2016-03-30Disabled Haplotype Analyst option if mapping scale is centimorgan/geneticzsloan
2016-03-30GN1 mapping now when mapping scale is centimorgan (for R/qtl)zsloan
Fixed some issues related to zooming in on chromosome X Fixed problem where it threw an error for mapping methods that didn't return additive effect Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome
2016-03-29Additive effect option now works for GN1 mapping figurezsloan
2016-03-29Forgot to add GeneralObject file needed for haplotype analyst in last commitzsloan
2016-03-29Haplotype Analyst now works for GN1 mapping figurezsloan
Chromosome drop-down select and Mb range text fields now are set to the values the user last selected
2016-03-28Legend option now works for GN1 mapping figurezsloan
2016-03-28Trait sample data table width now dynamically changes with number of ↵zsloan
attributes and standard error
2016-03-24Graph width can now be set in Mapping Resultszsloan
2016-03-24Add the Gene Track option to display the Gene Band for single chromosome viewzsloan
Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before)
2016-03-24Mapping results table is now limited to the top 200 markers; previously the ↵zsloan
page took a long time to load when there were too many markers
2016-03-23You can now select chromosome and an Mb range from the top menu and remapzsloan
The track in the single chromosome view to zoom into smaller intervals now works correctly again
2016-03-23Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan ↵zsloan
plot points are correct Table filters markers so it can always be displayed now (previously was too large for GEMMA)
2016-03-21Manhattan plot option now works for GN1 map, and GEMMA is set to display as ↵zsloan
manhattan plot
2016-03-21Changed code parsing marker csv file to increase GEMMA speedzsloan
Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this
2016-03-18Forgot to not retrieve sample data for the phenotype global search with the ↵zsloan
last commit, added it now
2016-03-18Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-18Replaced header with other information in qtl mapzsloan
Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
2016-03-17Fixed a bunch of geno files that had most of their contents removed for some ↵zsloan
reason
2016-03-15Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-03-15Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-03-15Fixed the mapping figure track that lets you zoom into a smaller rangezsloan
Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
2016-03-15Added mapping output file directory to gitignorezsloan
2016-03-14Changed the way headers look across all pageszsloan
Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-03Fixed issue where correlation would do mapping if run after mappingzsloan
2016-03-03Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-03-03Fixed trait export to include SE valueszsloan
2016-03-03Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 08:25:31 +0000