Refactor Locate Data Module #25
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roshankern
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Mar 9, 2023
* refactor locate data module (#25) * Idr stream module refactor (#26) * Co-authored-by: Jenna Tomkinson <jenna.tomkinson@ucdenver.edu> * add files for CP run * remove run cellpose plugin * refactor idrstreams * create python merge files * remove unecessary create folder line * docs * change conda environments with bash file * black formatting * Refactor format module (#27) * rerun module * rerun script * rerun notebook * greg suggestion * Refactor normalize module (#29) * rerun format module * refactor raw data umaps * update utils * run umaps notebook * reconvert jupyter notebook * normalize training data * rerun pipeline * jenna suggestions * Refactor umaps module (#30) * rerun notebook * docs, convert notebook * Update 4.analyze_data/README.md Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com> * documentation --------- Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com> * remove unecessary line from gitignore * fix typo * move constants outside of for loop --------- Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com>
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This PR is ready for review!
In this PR, the location data is formatted to be used with
idrstream_cp. This means that there is only one frame per line of location metadata (instead of multiple frames in one line of location metadata). Also, columns have been added to the location metadata forPlate_Map_Name,Gene_Replicate,Site, andDNA. The changes are shown below: