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2013-01-23Added a bunch to notes and created new notes file specifically...related to installing a new instance of GN Zachary Sloan
2013-01-22Added a couple things to notes regarding installing mysql clientZachary Sloan
2013-01-22Pushed through a few errors in getting the correlation page runningZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.py...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 Zachary Sloan
2013-01-11Commented out import of rpy2 in correlationFunction.py due to...problem with rpy2 Zachary Sloan
2013-01-11Upgraded packages requirements.txt but haven't testedZachary Sloan
2013-01-11Overwrote requirements.txtZachary Sloan
2013-01-11Trimmed a bunch of code off of marker_regression.pyZachary Sloan
2013-01-10Checking in before we try to write our own code for the manhattan...plot figure` Zachary Sloan
2013-01-10Checking in before trying to put manhattan plot sections closer togetherZachary Sloan
2013-01-10Normalized the y axis for each manhattan plot sectionZachary Sloan
2013-01-10The plots now correctly appear above/below each other....Committing before trying to combine all the manhattan plot segments Zachary Sloan
2013-01-10Edited marker_regression.coffee to make every sub-manhattan plot...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 Zachary Sloan
2013-01-10Made Chromosome class in marker_regression.coffee; current...it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that. Zachary Sloan
2013-01-10Made x-axis values into ints; committing before trying to add multiple graphs...for each chromosome Zachary Sloan
2013-01-10Worked with the manhattan plot coffeescript to set x-axis and change...the plot point sizes and remove lines Zachary Sloan
2013-01-09Manhattan plot results are appearing correctly for chromosome 1Zachary Sloan
2013-01-09The histogram coffeescript is now in its own class and the graph...still displays correctly Zachary Sloan
2013-01-09Checking in before putting the histogram coffeescript into its own...class Zachary Sloan
2013-01-09More or less finished the permutation histogramZachary Sloan
2013-01-09Got the permutation plot working as a line plot; still need to make...it into a bar graph, though Zachary Sloan
2013-01-09jqplot addedZachary Sloan
2013-01-09Got the marker regression page to display again...Passed lrs_array values as js_data for the permutation histogram Zachary Sloan
2013-01-08js_data is being printed out (seemingly) correctly now for the...marker_regression page Zachary Sloan
2013-01-08Created IndChromosome class in species.py and wrote functions for...chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs Zachary Sloan
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugs...Added a couple utility functions to the Chromosomes class in species.py Zachary Sloan
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2013-01-03Began working on marker_regression.py and created Chromosomes class...in species.py Zachary Sloan
2013-01-03marker_regression page is up againZachary Sloan
2013-01-03Created template for marek regression page and made the compute button direct...to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py Zachary Sloan
2012-12-20Changed layout of marker regression optionsZachary Sloan
2012-12-20The control locus field in the interval mapping settings is now disabled if..."choose closest control" is set to "yes" Zachary Sloan
2012-12-20Made composite mapping options show/hide for the interval mapping sectionZachary Sloan
2012-12-20More changes to the layout of interval mapping optionsZachary Sloan
2012-12-20Continued to customize the interval mapping menuZachary Sloan
2012-12-20Improved appearance/layout of the interval mapping tab using bootstrapZachary Sloan
2012-12-20Form data passed via POST for marker regression...Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan Zachary Sloan
2012-12-18Changed html for the marker regression tab...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" Zachary Sloan
2012-12-18Created new file species.py and species class object TheSpecies...Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests Zachary Sloan
2012-12-07Got links working for statistics table labelsZachary Sloan
2012-12-07Got basic statistics in show_trait to display the correct number...of samples for each group Got show_trait page to display for genotype traits Zachary Sloan
2012-12-07Got show_trait page to appear again for phenotype traits...Need to see why other samples list doesn't appear for traits in BXDPublishedPhenotypes Zachary Sloan
2012-12-06All 10 stats workingZachary Sloan
2012-12-06Continued work on basic statistics table in show_trait...Continued work towards getting show_trait to work with phenotype traits Zachary Sloan
2012-12-06Added minimum/maximum to basic statistics table...Continued bug-shooting related to getting show_trait running with phenotype traits Zachary Sloan
2012-12-06Got show_trait running again for MrnaAssay traitsZachary Sloan
2012-12-06Made many small changes to show_trait/data_set/search_results/trait to...remove use of the formData object and cursor Zachary Sloan
2012-12-05Renamed webqtlTrait.py to trait.py...Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough) Zachary Sloan
2012-12-05Continued to make changes related to getting rid of cursor/db_conn...and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again Zachary Sloan
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