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* wqflask/wqflask/static/new/packages/DataTables/: Delete folder.
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Removed some unused JS libraries
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https://github.com/genenetwork/genenetwork2/issues/310
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file format
Other changes include:
- Fixing links in the network graph
- Changing button colors on show trait page
- Changing color scheme for heatmap
- Making rows highlight in yellow when clicked on
- Some changes to table appearance (like giving gene global search a horizontal scroll)
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Improved appearance of search result and collection tables
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- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits
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Temporarily removed second sample table for CFW traits
Fixed location of global search bar to work with wider screens
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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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Updated dataset_menu_structure.json
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be there and changed the code that calls them accordingly
Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)
Removed some unused code from show_trait.py
changed appearance of table headers some, though needs a little more work
Updated dataset_menu_structure.json
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Automatically determines number of decimal places to show on y axis of probability plot; still need to figure out how to do it with bar chart
Added some logging to figure out MySQL connection issue
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former) and made all tables a little more compact by lessenning the padding
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of the page (still not totally pleased with them though)
Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
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- Wrong digits for mean expression and additive effect
- Bad loooking width on some columns, like Max LRS Location
- Janky functionality for column resizing and drag-and-dropping (just disabled these functions)
- Geno and Pheno global search tables weren't built in the same way, so now they are
I also fixed the sorting to always put N/A's at the bottom of the table by editing naturalSort.js
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Fixed a couple minor html syntax erors in login_user.html and base.html
Changed export button on correlation page to csvHtml5, but still has problem with commas in fields being interpreted as a new column
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some corresponding imports
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column resizing on global search pages
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tables and later attach its functionality to the existing Download Table button
Fixed an issue where rows wouldn't uncheck with backspacing in Select Top text area;
the last commit just fixed the highlighting, not the checkboxes
Some changes in progress towards trying to fix the additive effect issue; the problem is
that the lod_chart.js code writes each chromosome as one d3 path, so I can't change the color
for individual segments within that path. I'll have to completely change the way
the path is drawn for the additive effect
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for all of them, among other minor changes
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select top)
Search table and Select Top options added to global and regular search pages
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Made some more changes/improvements to various tables throughout the site
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more issues to resolve, like setting initial column width
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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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added informative tooltips and error bars
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* z scores are computed on the client side (using jStat library)
* added Shapiro-Wilk test results
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I figure out how to get it to read the port from the config file instead
Using runserver.py instead of secure_server.py because of an error with the latter
that I haven't figured out how to fix yet
Improved the appearance of several of the tables
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Started creating probability plot for show trait page
Added outlier detection message when user does mapping
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adding the correlation matrix page
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the trait page
Hid the Quick Search on the index page until it is working well.
Started writing a file to run the pyLMM code in the background to
avoid memory issues/timing out
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for all of our genofiles
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Downloaded jquery validation code to use with the block index feature
on the trait data page (as well as others in the future).
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