genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2014-05-05	Committing a bunch of changes related to integrating GEMMA and	Zachary Sloan
	adding the correlation matrix page
2014-03-26	Got anonymous collections working correctly	Zachary Sloan
	Got results for the HSNIH and CANDLE marker regression pages (still some issues with the manhattan plot)
2014-02-28	Committing after creating AnonCollection class and before adding	Zachary Sloan
	remove trait function
2014-02-28	Made some changes/comments to Lei's load_genotypes.py file	Zachary Sloan

2014-02-27	Began working on a TraitCollection.py file that will contain both the	Zachary Sloan
	object for logged in user collections and collections created by anonymous users.
2014-02-26	Collection page now displays for temp/anon collections, but	Zachary Sloan
	still needs the option to remove traits from them
2014-02-25	Made some more progress towards getting anonymous collections working	Zachary Sloan

2014-02-25	Committing part-way through getting anonymous collections working	Zachary Sloan

2014-02-25	Merge /home/sam/gene	Zachary Sloan

2014-02-25	Added untracked file	Sam

2014-02-25	Just committing after messing with the marker regression plot	Zachary Sloan

2014-02-24	Chromosome zoom is working for the marker regression manhattan plot	Zachary Sloan
	and results show up correctly in the table again
2014-01-30	The calculations for the manhattan plot are now run from the command	Zachary Sloan
	line as a background process, allowing multiple to be run at the same time without the time increasing.
2014-01-30	Added forgotten html page to repo	Sam
	Fixed bugs where- - User tried to login with an email address that hasn't been registered - User tries to register an email address that was already registered Testing is still needed to confirm bugs were fixed properly and new ones weren't introduced
2014-01-30	Before trying to fix user login issue	Sam

2014-01-30	Most of the work is done towards running lmm.py from the command line	Zachary Sloan
	and storing the results in redis
2014-01-29	Limited number of markers in marker regression result table to	Zachary Sloan
	those with a lod score > 2 Did some work towards adding the colored backgrounds to chromosome areas in the manhattan plot Changed the last two chromosomes for human manhattan plots to X and X/Y Started work on writing a script that can independently run the pyLMM code and store the results in redis
2014-01-24	Added natural sort to sort the index column for the sample data in	Zachary Sloan
	the trait page Hid the Quick Search on the index page until it is working well. Started writing a file to run the pyLMM code in the background to avoid memory issues/timing out
2014-01-23	Histogram is working	Zachary Sloan
	Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03	Wrote some code for the histogram figure	Zachary Sloan
	Changed some code in dataset to try and track down the issue with Amelie's file
2013-12-31	Finished code to remove a trait or multiple traits from a collection	Sam
	Wrote code to make buttons a little cleaner and more obvious when dealing with collections (they now enable themselves when traits that can be added or removed to/from a collection are selected)
2013-12-30	Fixed issue where box plots initially appeared below the bar chart	Zachary Sloan
	instead of in the second tab In the process of trying to fix the genofile to json parser so we can map Amelie's rat data In the process of having the color of bars in the bar chart "follow" them when they are resorted.
2013-12-30	Collections changes	Sam

2013-12-18	Merge /home/zas1024/gene	Sam

2013-12-18	Fixed issue where "Type" and "Dataset" had no default values for	Zachary Sloan
	the home page drop-downs
2013-12-17	Added the option to choose which method to use for the interval	Zachary Sloan
	mapping function (pyLMM or qtl reaper)
2013-12-12	Put the code that rebuilds the bar chart into a function	Zachary Sloan
	Still need to fix issue where attribute colors don't stay with their associated samples/strains
2013-12-11	Got sort by name/value buttons working and committing before trying	Zachary Sloan
	to put some of the d3 code into a function
2013-12-11	Got color by trait working, but still need to add a legend and make	Zachary Sloan
	some other small changes (like removing samples that don't overlap with the selected trait) Tentatively removed jquery-ui from base.html; I'm not sure if we're still using this anywhere, but removing it doesn't seem to have had an impact on the trait page
2013-12-05	Now trims selected trait's values by the samples of the primary trait and	Zachary Sloan
	gets their distinct values Created function that creates a dictionary of distinct values and their corresponding colors
2013-12-05	Interval map graph now works properly	Zachary Sloan
	Tried to export trait data for "color by trait" function
2013-11-28	Adding to collection now shows collection you added to and has informative ↵	Sam
	message as to how many traits added.
2013-11-27	Clicking a trait in "color by trait" now gets all of its sample values	Zachary Sloan
	that will be used to color the bar graph
2013-11-27	Can now view trait list of a collection after clicking the collection	Zachary Sloan
	in the modal that pops up after clicking "Color by Trait" above the bar chart
2013-11-26	Made some progress towards getting the traits inside a collection to display ↵	Zachary Sloan
	on hover
2013-11-25	Added HSNIH.json to ignore due to its size	Zachary Sloan

2013-11-25	Merge branch 'temp'	Zachary Sloan

2013-11-25	Got the interval mapping results into a table	Zachary Sloan

2013-11-22	Did some work towards getting the interval mapping page working	Zachary Sloan

2013-11-21	Added apt-get dist-upgrade to notes	Zachary Sloan

2013-11-20	Merge /home/zas1024/gene	Lei Yan

2013-11-20	Created a box plot	Zachary Sloan
	Made the bar chart use a gradient if colored by something with more than 6 distinct values Put figures in tabs under the Charts/Figures part of the trait page
2013-11-14	Can change the parameters of Sample Correlation Scatterplot	Lei Yan

2013-11-05	Merge /home/zas1024/gene	Lei Yan
	Conflicts: wqflask/wqflask/templates/correlation_page.html
2013-11-05	Add Correlation Scatter plot	Lei Yan

2013-11-01	In the process of opening a modal with the collection page inside	Zachary Sloan

2013-11-01	In the process of adding the function to color bar chart by the	Zachary Sloan
	values of a trait in your collection
2013-11-01	Merge /home/sam/gene	Zachary Sloan

2013-11-01	Made the extra attribute bar chart coloring continue to work	Zachary Sloan
	when the user sorts and gave the option to revert to no coloring
2013-10-31	Refactored login code and got remember me working	Sam