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* wqflask/utility/Plot.py: import corestats from the utility module.
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* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is
does not have py3 support so it's important to remove references to it.
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
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* wqflask/utility/Plot.py: Update docstring.
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Use the new draw_rotated_text() function to draw the text rotated as was
formerly done.
* wqflask/utility/Plot.py (plotBar): Use draw_rotated_text().
* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults) Use draw_rotated_text().
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* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Add font files
(DisplayMappingResults): Update the code from the Piddle way of things to the
Pillow way of things, for example, replace:
- pid.drawRect(...) with im_drawer.rectangle(...)
- pid.drawString(...) with im_drawer.text(...)
- pid.drawPolygon(...) with im_drawer.polygon(...) etc.
* wqflask/utility/Plot.py: Migrate code from the older, unsupported Piddle to
the newer Pillow library.
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Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
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pretty sure also isn't used any more.
Also removed some other unused code from the files listed
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variable not being initialized
Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them.
Also removed unused file AJAX_table.py and other unused code from several other files
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being used except corestats, which I moved to utility
Removed box plot code from Plot.py since we no longer use it either
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Fixed typo in show_trait html that caused the p-value slider to not work for correlations
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now work for both R/qtl and qtl reaper mapping.
Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome)
Added text below figure when Allele Effects selected/relevant
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generated in Jinja2
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