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Added data_scale to dataset objects and basic stats table will now check data scale when calculating range
Made interval analyst results table work with datatables
Changed the appearance of the basic stats table some by giving it a border
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chromosome view for mapping results
Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
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isn't checked (it used to just "connect the dots" of the marker regression output)
Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
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the last commit)
Fixed order of stats table in trait page
Removed the qtl results table from chromosome view; will add the Interval Analyst output later
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chromosomes
Added text explaining what * indicates in the mapping options menu
Removed ranges (log2 and fold) from stats table for phenotype traits
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error for phenotype traits
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gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py)
This change increases the speed by a bit (85 seconds to 66 seconds for example)
Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
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mapping scale (lrs or lod)
Fixed bug where broken image link would appear if you ran R/qtl with no permutations
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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 correctly.
The correct value (LRS or LOD) will now be displayed in the results table
Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
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display LOD scores for the Y-Axis instead of LRS values
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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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full genome view
There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
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genetic(centimorgan) mapping
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Fixed some issues related to zooming in on chromosome X
Fixed problem where it threw an error for mapping methods that didn't return additive effect
Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome
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Chromosome drop-down select and Mb range text fields now are set to the values the user last selected
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attributes and standard error
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Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before)
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page took a long time to load when there were too many markers
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The track in the single chromosome view to zoom into smaller intervals now works correctly again
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plot points are correct
Table filters markers so it can always be displayed now (previously was too large for GEMMA)
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manhattan plot
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Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this
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last commit, added it now
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Began adding menu to qtl map
Fixed global search to not retrieve samples (to increase speed)
Got the vector plot working again so it can be displayed alongside the gn1-style plot
Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
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Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
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Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
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Still slower than preferable due to having to query the gn1 database for every trait in the search results
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collections list, collection view, gene/pheno global search, and regular search
Not sure what the best way to determine the filename is, so just using "search_results" or "collection_list" for now
In future I want to replace the default csv download button by attaching its function to the previous "Download Table" button
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Updated dataset menu structure json
Increased the width for the label and text field for inputting MAF for PLINK and GEMMA
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the y scale
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