genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-02-13	Fixed some bugs related to getting the marker regression page working	Zachary Sloan
	with Nick's code
2013-02-12	Edited marker_regression.py and data_set.py to store the p-values	Zachary Sloan
	and their corresponding markers to be used in the table of qtl results and other figures
2013-02-08	Converted .geno files to json files and wrote code in marker_regression.py	Zachary Sloan
	that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running)
2013-02-07	Added code to marker_regression.py that creates the numpy arrays to	Zachary Sloan
	pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited
2013-02-06	Edited genofile_parser.py to go through all genofiles and convert	Zachary Sloan
	them to the format used by nick's code
2013-02-06	Added changes to example.py and prep_data.py that lets nick's code read in	Zachary Sloan
	our data
2013-02-06	Small change to search_results.py to get search results page to work	Zachary Sloan

2013-01-31	Added wqflask-nginx.conf	Zachary Sloan

2013-01-31	Copied over nginx.conf from /etc/nginx	Zachary Sloan

2013-01-31	Merge branch 'flask' of https://github.com/zsloan/genenetwork into flask	Zachary Sloan

2013-01-31	Changed reference to 'dataset_name' in keywords to 'dataset' to get	Zachary Sloan
	page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object
2013-01-31	Changed fd to kw in search_results.py, commented out some lines	Zachary Sloan
	related to fd
2013-01-25	Fixed a few bugs while trying to get the code running on the new server	Zachary Sloan

2013-01-22	Pushed through a few errors in getting the correlation page running	Zachary Sloan

2013-01-18	Renamed CorrelationPage.py to show_corr_results.py	Zachary Sloan
	Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-11	Commented out import of rpy2 in correlationFunction.py due to	Zachary Sloan
	problem with rpy2
2013-01-11	Upgraded packages requirements.txt but haven't tested	Zachary Sloan

2013-01-11	Overwrote requirements.txt	Zachary Sloan

2013-01-11	Trimmed a bunch of code off of marker_regression.py	Zachary Sloan

2013-01-10	Checking in before we try to write our own code for the manhattan	Zachary Sloan
	plot figure`
2013-01-10	Checking in before trying to put manhattan plot sections closer together	Zachary Sloan

2013-01-10	Normalized the y axis for each manhattan plot section	Zachary Sloan

2013-01-10	The plots now correctly appear above/below each other.	Zachary Sloan
	Committing before trying to combine all the manhattan plot segments
2013-01-10	Edited marker_regression.coffee to make every sub-manhattan plot	Zachary Sloan
	for each chromosome display Created css file for the marker_regression page Currently has display issue where the permutation histogram is overlapping with the manhattan plot
2013-01-10	Made Chromosome class in marker_regression.coffee; current	Zachary Sloan
	it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that.
2013-01-10	Made x-axis values into ints; committing before trying to add multiple graphs	Zachary Sloan
	for each chromosome
2013-01-10	Worked with the manhattan plot coffeescript to set x-axis and change	Zachary Sloan
	the plot point sizes and remove lines
2013-01-09	Manhattan plot results are appearing correctly for chromosome 1	Zachary Sloan

2013-01-09	The histogram coffeescript is now in its own class and the graph	Zachary Sloan
	still displays correctly
2013-01-09	Checking in before putting the histogram coffeescript into its own	Zachary Sloan
	class
2013-01-09	More or less finished the permutation histogram	Zachary Sloan

2013-01-09	Got the permutation plot working as a line plot; still need to make	Zachary Sloan
	it into a bar graph, though
2013-01-09	jqplot added	Zachary Sloan

2013-01-09	Got the marker regression page to display again	Zachary Sloan
	Passed lrs_array values as js_data for the permutation histogram
2013-01-08	js_data is being printed out (seemingly) correctly now for the	Zachary Sloan
	marker_regression page
2013-01-08	Created IndChromosome class in species.py and wrote functions for	Zachary Sloan
	chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08	Deleted some unnecessary code in marker_regression.py and fixed some bugs	Zachary Sloan
	Added a couple utility functions to the Chromosomes class in species.py
2013-01-04	Continued rewriting marker_regression.py code	Zachary Sloan

2013-01-04	Correct results are being returned from reaper for the marker regression page	Zachary Sloan

2013-01-03	Began working on marker_regression.py and created Chromosomes class	Zachary Sloan
	in species.py
2013-01-03	marker_regression page is up again	Zachary Sloan

2013-01-03	Created template for marek regression page and made the compute button direct	Zachary Sloan
	to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-20	Changed layout of marker regression options	Zachary Sloan

2012-12-20	The control locus field in the interval mapping settings is now disabled if	Zachary Sloan
	"choose closest control" is set to "yes"
2012-12-20	Made composite mapping options show/hide for the interval mapping section	Zachary Sloan

2012-12-20	More changes to the layout of interval mapping options	Zachary Sloan

2012-12-20	Continued to customize the interval mapping menu	Zachary Sloan

2012-12-20	Improved appearance/layout of the interval mapping tab using bootstrap	Zachary Sloan

2012-12-20	Form data passed via POST for marker regression	Zachary Sloan
	Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan
2012-12-18	Changed html for the marker regression tab	Zachary Sloan
	Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form"