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Various changes/fixes
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files and how it writes the phenotype file)
Y-axis for GEMMA now says -log(p)
Updated the style of the trait sample data table in the trait page
Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs)
Updated dataset menu json file
Added option to show and hide columns to regular search page using colVis
Changed regular and global search result table styles/column widths
Began work on user trait submission code (not working yet though)
Began work on static loading page for mapping results
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Various changes
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(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
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increases table load speed
In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip
Increased table width for non-Geno DBs
Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches
Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little
Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
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settings
Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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fetch1 to return a tuple
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names (like BXD65a)
R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
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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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[PATCH 039/100] Removing commented code
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[PATCH 038/100] Fix compile errors
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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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Still slower than preferable due to having to query the gn1 database for every trait in the search results
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not work because of the new dataset_menu_structure.json file
An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
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pylmm was wrong
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Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
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phenotype)
Fixed issue where LRS and LOD are sometimes labeled incorrectly
Changed the header of the trait page
Added link to GN1 in header
Fixxed an issue that made permutations not work with pylmm
Fixed "sign in" button when creating a collection while not logged in
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Made changes to the tables of correlation results, collections, and search results:
- Added resizeable columns to correlation results and collections, but not to search results
because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling
to the search results)
- Correlation results and collections are now in scrolling tables
- The style is the same across all of these tables now
Remaining issues:
- It doesn't seem like I can set the column width when initializing dataTables in
correlation results. I don't know why this is; it might be due to the table already being the size
of a full page. I want to be able to default to some good widths, even if the user can resize them
- I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is
due to having to put the text in a div.
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incorrectly converted to json
Fixed GO search to work with combined searches
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Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
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Fixes #69
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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