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2013-02-15Created lines in marker regression scatter plot separatingZachary Sloan
chromosomes
2013-02-14Put coffeescript code for manhattan plot into a class/functionsZachary Sloan
2013-02-14Have marker regression results displaying as a scatterplot (just the points)Zachary Sloan
using d3.js
2013-02-13Got results displaying for BXD and fixed genofile_parser.py to workZachary Sloan
for all of our genofiles
2013-02-13Got results for marker regression page displaying in tableZachary Sloan
2013-02-13Fixed some bugs related to getting the marker regression page workingZachary Sloan
with Nick's code
2013-02-12Edited marker_regression.py and data_set.py to store the p-valuesZachary Sloan
and their corresponding markers to be used in the table of qtl results and other figures
2013-02-08Converted .geno files to json files and wrote code in marker_regression.pyZachary 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)
2013-02-07Added code to marker_regression.py that creates the numpy arrays toZachary 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
2013-02-06Edited genofile_parser.py to go through all genofiles and convertZachary Sloan
them to the format used by nick's code
2013-02-06Added changes to example.py and prep_data.py that lets nick's code read inZachary Sloan
our data
2013-02-06Small change to search_results.py to get search results page to workZachary Sloan
2013-01-31Added wqflask-nginx.confZachary Sloan
2013-01-31Copied over nginx.conf from /etc/nginxZachary Sloan
2013-01-31Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Deleted nginx.conf from the other_conf directory not in wqflaskZachary Sloan
2013-01-31Merge branch 'flask' of https://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Changed reference to 'dataset_name' in keywords to 'dataset' to getZachary 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
2013-01-31Changed fd to kw in search_results.py, commented out some linesZachary Sloan
related to fd
2013-01-25Added a bunch of things to notesZachary Sloan
2013-01-25Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-25Fixed a few bugs while trying to get the code running on the new serverZachary Sloan
2013-01-24Added a lot to the notes in the process of setting up on theZachary Sloan
new server
2013-01-23Added a bunch to notes and created new notes file specificallyZachary Sloan
related to installing a new instance of GN
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.pyZachary 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
2013-01-11Commented out import of rpy2 in correlationFunction.py due toZachary Sloan
problem with rpy2
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 manhattanZachary Sloan
plot figure`
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.Zachary Sloan
Committing before trying to combine all the manhattan plot segments
2013-01-10Edited marker_regression.coffee to make every sub-manhattan plotZachary 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
2013-01-10Made Chromosome class in marker_regression.coffee; currentZachary Sloan
it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that.
2013-01-10Made x-axis values into ints; committing before trying to add multiple graphsZachary Sloan
for each chromosome
2013-01-10Worked with the manhattan plot coffeescript to set x-axis and changeZachary Sloan
the plot point sizes and remove lines
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 graphZachary Sloan
still displays correctly
2013-01-09Checking in before putting the histogram coffeescript into its ownZachary Sloan
class
2013-01-09More or less finished the permutation histogramZachary Sloan
2013-01-09Got the permutation plot working as a line plot; still need to makeZachary Sloan
it into a bar graph, though
2013-01-09jqplot addedZachary Sloan
2013-01-09Got the marker regression page to display againZachary Sloan
Passed lrs_array values as js_data for the permutation histogram
2013-01-08js_data is being printed out (seemingly) correctly now for theZachary Sloan
marker_regression page
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
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