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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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in species.py
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to it
added asbolute_import in data_set.py and trait.py
Made several minor changes and deleted commented out code in trait.py
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"choose closest control" is set to "yes"
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