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2014-07-18Forgot to add the heatmap __init__.py file in the last commitZachary Sloan
2014-07-18Just did some more work on the heatmapZachary Sloan
2014-07-18Added outlier highlightingZachary Sloan
Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-14Made interval map zoom look betterZachary Sloan
Started creating probability plot for show trait page Added outlier detection message when user does mapping
2014-07-09Updated coffeescript, svg export working fine, interval mapping zoom workingZachary Sloan
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-12Long overdue of commit to changes that add a scatter plot to the correlation ↵Zachary Sloan
page and let you select a trait from your collection on the trait page and do a scatter plot against that triat as well. There are a number of accompanying js and css files written by Karl Broman that are needed for these features. The option to compare against more than just one trait still needs to be added for the trait page scatterplot function
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added
2014-05-19Fixed sorting on the show trait pageZachary Sloan
Added/improved the x and y axis on the bar graph and histogram GEMMA working but still really slow
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-03-26Got anonymous collections working correctlyZachary Sloan
Got results for the HSNIH and CANDLE marker regression pages (still some issues with the manhattan plot)
2014-02-28Committing after creating AnonCollection class and before addingZachary Sloan
remove trait function
2014-02-28Made some changes/comments to Lei's load_genotypes.py fileZachary Sloan
2014-02-27Began working on a TraitCollection.py file that will contain both theZachary Sloan
object for logged in user collections and collections created by anonymous users.
2014-02-26Collection page now displays for temp/anon collections, butZachary Sloan
still needs the option to remove traits from them
2014-02-25Made some more progress towards getting anonymous collections workingZachary Sloan
2014-02-25Committing part-way through getting anonymous collections workingZachary Sloan
2014-02-25Merge /home/sam/geneZachary Sloan
2014-02-25Added untracked fileSam
2014-02-25Just committing after messing with the marker regression plotZachary Sloan
2014-02-24Chromosome zoom is working for the marker regression manhattan plotZachary Sloan
and results show up correctly in the table again
2014-01-30The calculations for the manhattan plot are now run from the commandZachary Sloan
line as a background process, allowing multiple to be run at the same time without the time increasing.
2014-01-30Added forgotten html page to repoSam
Fixed bugs where- - User tried to login with an email address that hasn't been registered - User tries to register an email address that was already registered Testing is still needed to confirm bugs were fixed properly and new ones weren't introduced
2014-01-30Before trying to fix user login issueSam
2014-01-30Most of the work is done towards running lmm.py from the command lineZachary Sloan
and storing the results in redis
2014-01-29Limited number of markers in marker regression result table toZachary Sloan
those with a lod score > 2 Did some work towards adding the colored backgrounds to chromosome areas in the manhattan plot Changed the last two chromosomes for human manhattan plots to X and X/Y Started work on writing a script that can independently run the pyLMM code and store the results in redis
2014-01-24Added natural sort to sort the index column for the sample data inZachary Sloan
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
2014-01-23Histogram is workingZachary Sloan
Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03Wrote some code for the histogram figureZachary Sloan
Changed some code in dataset to try and track down the issue with Amelie's file
2013-12-31Finished code to remove a trait or multiple traits from a collectionSam
Wrote code to make buttons a little cleaner and more obvious when dealing with collections (they now enable themselves when traits that can be added or removed to/from a collection are selected)
2013-12-30Fixed issue where box plots initially appeared below the bar chartZachary Sloan
instead of in the second tab In the process of trying to fix the genofile to json parser so we can map Amelie's rat data In the process of having the color of bars in the bar chart "follow" them when they are resorted.
2013-12-30Collections changesSam
2013-12-18Merge /home/zas1024/geneSam
2013-12-18Fixed issue where "Type" and "Dataset" had no default values forZachary Sloan
the home page drop-downs
2013-12-17Added the option to choose which method to use for the intervalZachary Sloan
mapping function (pyLMM or qtl reaper)
2013-12-12Put the code that rebuilds the bar chart into a functionZachary Sloan
Still need to fix issue where attribute colors don't stay with their associated samples/strains
2013-12-11Got sort by name/value buttons working and committing before tryingZachary Sloan
to put some of the d3 code into a function
2013-12-11Got color by trait working, but still need to add a legend and makeZachary Sloan
some other small changes (like removing samples that don't overlap with the selected trait) Tentatively removed jquery-ui from base.html; I'm not sure if we're still using this anywhere, but removing it doesn't seem to have had an impact on the trait page
2013-12-05Now trims selected trait's values by the samples of the primary trait andZachary Sloan
gets their distinct values Created function that creates a dictionary of distinct values and their corresponding colors
2013-12-05Interval map graph now works properlyZachary Sloan
Tried to export trait data for "color by trait" function
2013-11-28Adding to collection now shows collection you added to and has informative ↵Sam
message as to how many traits added.
2013-11-27Clicking a trait in "color by trait" now gets all of its sample valuesZachary Sloan
that will be used to color the bar graph
2013-11-27Can now view trait list of a collection after clicking the collectionZachary Sloan
in the modal that pops up after clicking "Color by Trait" above the bar chart
2013-11-26Made some progress towards getting the traits inside a collection to display ↵Zachary Sloan
on hover
2013-11-25Merge branch 'temp'Zachary Sloan
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-11-22Did some work towards getting the interval mapping page workingZachary Sloan
2013-11-20Merge /home/zas1024/geneLei Yan
2013-11-20Created a box plotZachary Sloan
Made the bar chart use a gradient if colored by something with more than 6 distinct values Put figures in tabs under the Charts/Figures part of the trait page
2013-11-14Can change the parameters of Sample Correlation ScatterplotLei Yan
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