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using d3.js
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for all of our genofiles
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with Nick's code
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and their corresponding markers to be used in the table of qtl results
and other figures
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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)
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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
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them to the format used by nick's code
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our data
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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
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related to fd
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new server
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related to installing a new instance of GN
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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
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problem with rpy2
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plot figure`
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Committing before trying to combine all the manhattan plot
segments
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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
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it writes each chromosome's manhattan plot on top of each
other. This commit is before trying to fix that.
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for each chromosome
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the plot point sizes and remove lines
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still displays correctly
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class
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it into a bar graph, though
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Passed lrs_array values as js_data for the permutation histogram
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marker_regression page
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chromosome-related attributes
Began to try and pass qtlreaper results as js_data to use when
drawing graphs
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Added a couple utility functions to the Chromosomes class in species.py
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