| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2014-06-12 | Long 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 | |||
| 2014-06-06 | Implimented Karl Broman's lodchart code for the interval mapping function. | Zachary Sloan | |
| Suggestive/significant bars and additive effect curve added | |||
| 2014-05-19 | Fixed sorting on the show trait page | Zachary Sloan | |
| Added/improved the x and y axis on the bar graph and histogram GEMMA working but still really slow | |||
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and | Zachary Sloan | |
| adding the correlation matrix page | |||
| 2014-03-26 | Got anonymous collections working correctly | Zachary Sloan | |
| Got results for the HSNIH and CANDLE marker regression pages (still some issues with the manhattan plot) | |||
| 2014-02-28 | Committing after creating AnonCollection class and before adding | Zachary Sloan | |
| remove trait function | |||
| 2014-02-28 | Made some changes/comments to Lei's load_genotypes.py file | Zachary Sloan | |
| 2014-02-27 | Began working on a TraitCollection.py file that will contain both the | Zachary Sloan | |
| object for logged in user collections and collections created by anonymous users. | |||
| 2014-02-26 | Collection page now displays for temp/anon collections, but | Zachary Sloan | |
| still needs the option to remove traits from them | |||
| 2014-02-25 | Made some more progress towards getting anonymous collections working | Zachary Sloan | |
| 2014-02-25 | Committing part-way through getting anonymous collections working | Zachary Sloan | |
| 2014-02-25 | Merge /home/sam/gene | Zachary Sloan | |
| 2014-02-25 | Added untracked file | Sam | |
| 2014-02-25 | Just committing after messing with the marker regression plot | Zachary Sloan | |
| 2014-02-24 | Chromosome zoom is working for the marker regression manhattan plot | Zachary Sloan | |
| and results show up correctly in the table again | |||
| 2014-01-30 | The calculations for the manhattan plot are now run from the command | Zachary Sloan | |
| line as a background process, allowing multiple to be run at the same time without the time increasing. | |||
| 2014-01-30 | Added forgotten html page to repo | Sam | |
| 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 | |||
| 2014-01-30 | Before trying to fix user login issue | Sam | |
| 2014-01-30 | Most of the work is done towards running lmm.py from the command line | Zachary Sloan | |
| and storing the results in redis | |||
| 2014-01-29 | Limited number of markers in marker regression result table to | Zachary 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 | |||
| 2014-01-24 | Added natural sort to sort the index column for the sample data in | Zachary 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 | |||
| 2014-01-23 | Histogram is working | Zachary Sloan | |
| Fixed some bug with generating the manhattan plot for the HLC data set | |||
| 2014-01-03 | Wrote some code for the histogram figure | Zachary Sloan | |
| Changed some code in dataset to try and track down the issue with Amelie's file | |||
| 2013-12-31 | Finished code to remove a trait or multiple traits from a collection | Sam | |
| 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) | |||
| 2013-12-30 | Fixed issue where box plots initially appeared below the bar chart | Zachary 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. | |||
| 2013-12-30 | Collections changes | Sam | |
| 2013-12-18 | Merge /home/zas1024/gene | Sam | |
| 2013-12-18 | Fixed issue where "Type" and "Dataset" had no default values for | Zachary Sloan | |
| the home page drop-downs | |||
| 2013-12-17 | Added the option to choose which method to use for the interval | Zachary Sloan | |
| mapping function (pyLMM or qtl reaper) | |||
| 2013-12-12 | Put the code that rebuilds the bar chart into a function | Zachary Sloan | |
| Still need to fix issue where attribute colors don't stay with their associated samples/strains | |||
| 2013-12-11 | Got sort by name/value buttons working and committing before trying | Zachary Sloan | |
| to put some of the d3 code into a function | |||
| 2013-12-11 | Got color by trait working, but still need to add a legend and make | Zachary 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 | |||
| 2013-12-05 | Now trims selected trait's values by the samples of the primary trait and | Zachary Sloan | |
| gets their distinct values Created function that creates a dictionary of distinct values and their corresponding colors | |||
| 2013-12-05 | Interval map graph now works properly | Zachary Sloan | |
| Tried to export trait data for "color by trait" function | |||
| 2013-11-28 | Adding to collection now shows collection you added to and has informative ↵ | Sam | |
| message as to how many traits added. | |||
| 2013-11-27 | Clicking a trait in "color by trait" now gets all of its sample values | Zachary Sloan | |
| that will be used to color the bar graph | |||
| 2013-11-27 | Can now view trait list of a collection after clicking the collection | Zachary Sloan | |
| in the modal that pops up after clicking "Color by Trait" above the bar chart | |||
| 2013-11-26 | Made some progress towards getting the traits inside a collection to display ↵ | Zachary Sloan | |
| on hover | |||
| 2013-11-25 | Merge branch 'temp' | Zachary Sloan | |
| 2013-11-25 | Got the interval mapping results into a table | Zachary Sloan | |
| 2013-11-22 | Did some work towards getting the interval mapping page working | Zachary Sloan | |
| 2013-11-20 | Merge /home/zas1024/gene | Lei Yan | |
| 2013-11-20 | Created a box plot | Zachary 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 | |||
| 2013-11-14 | Can change the parameters of Sample Correlation Scatterplot | Lei Yan | |
| 2013-11-05 | Merge /home/zas1024/gene | Lei Yan | |
| Conflicts: wqflask/wqflask/templates/correlation_page.html | |||
| 2013-11-05 | Add Correlation Scatter plot | Lei Yan | |
| 2013-11-01 | In the process of opening a modal with the collection page inside | Zachary Sloan | |
| 2013-11-01 | In the process of adding the function to color bar chart by the | Zachary Sloan | |
| values of a trait in your collection | |||
| 2013-11-01 | Merge /home/sam/gene | Zachary Sloan | |
| 2013-11-01 | Made the extra attribute bar chart coloring continue to work | Zachary Sloan | |
| when the user sorts and gave the option to revert to no coloring | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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