1. 11 Jul, 2021 2 commits
    • Ryoko's avatar
      Moved scikit-learn clusterings to separate folder · b5fdc436
      Ryoko authored
      To separate from the borrowed notebooks, put the clustering notebooks in a separate folder: scikit_clusterings.
      This folder contains
      - scikit_kmeans.ipynb
      - plot_fig1c.py
      - preprocess_figdata.py
      b5fdc436
    • Ryoko's avatar
      Created a module for plotting · 4c7d5e7c
      Ryoko authored
      plot_fig1c.py allows you to plot figure 1c without copy-pasting cells from the original notebooks. It also has a function to plot figure1c's t-SNE representations colored with new cluster assignments, with the original figure 1c at its side for reference.
      4c7d5e7c
  2. 10 Jul, 2021 4 commits
    • Ryoko's avatar
      Fixed minor typos · b6ca1a87
      Ryoko authored
      Fixed minor typos in about_figure_1c.ipynb
      b6ca1a87
    • Ryoko's avatar
      Added notebook for experimenting k-means · 1a943b9c
      Ryoko authored
      Added a notebook for experimenting with k-means and the data in figure 1c. viplamp_exint.pickle and viplamp_umi.pickle are the files created after preprocessing.
      1a943b9c
    • Ryoko's avatar
      Added code for preprocessing · 69d1f5b7
      Ryoko authored
      preprocess_figdata.py preprocesses transcriptomic count data in the same way as written in the article
      69d1f5b7
    • Ryoko's avatar
      Corrected minor typos · 4bd7ac22
      Ryoko authored
      Corrected minor typos in about_figure_1c.ipynb
      4bd7ac22
  3. 09 Jul, 2021 1 commit
    • Ryoko's avatar
      Corrected information about UMI counts · 9273921b
      Ryoko authored
      After reading the paper again, found that what I thought was gene counts actually was UMI counts. So I corrected the information in about_figure_1c.ipynb.
      9273921b
  4. 07 Jul, 2021 1 commit
    • Ryoko's avatar
      Finalized about_figure_1c · c2fb76c2
      Ryoko authored
      Changed the file name of understanding_image_1c.ipynb to about_figure_1c.ipynb.
      
      Organized understanding so it is more readable.
      c2fb76c2
  5. 05 Jul, 2021 2 commits
  6. 03 Jul, 2021 1 commit
  7. 02 Jul, 2021 1 commit
  8. 01 Jul, 2021 2 commits
  9. 30 Jun, 2021 2 commits
    • Ryoko's avatar
      Added summary of original article · 494a1654
      Ryoko authored
      Added a summary of the article by Scala et al. to understanding_image_1c. Also added the summary of a previous research by Tasic et al. that Scala referred to. Started writing the summary of another reference article by Yao et al. but not finished yet.
      494a1654
    • Ryoko's avatar
      Corrected plotting error · 5bdc4ba9
      Ryoko authored
      Found out that the name error you get for "L5 ET_1" actually meant "L5 PT_1" according to the study by Yao et al. Made corrections for that in the plotting code.
      5bdc4ba9
  10. 29 Jun, 2021 1 commit
    • Ryoko's avatar
      Started interpreting image 1c · 59e8cdc8
      Ryoko authored
      Created a notebook dedicated to understanding image 1c. I created the notebook by changing the name of a notebook I intended to use for clustering (which was still enpty).
      59e8cdc8
  11. 25 Jun, 2021 1 commit
    • Ryoko's avatar
      Changed name and executed ttype-coverage · 7a991f3a
      Ryoko authored
      Added descriptions and commented out a line that no longer works in ttype-coverage.ipynb. The reason for commenting out the line can be found in the notebook. Changed the file name because it's no longer the original.
      
      The commented out line was like this:
      col = clusterColors[clusterNames=='L5 ET_1'][0] 
      
      Ran the file to see if it works, and in the process created the "extra" directory and "mainfigures" directory in figures because the notebook writes 
      images there.
      7a991f3a
  12. 23 Jun, 2021 1 commit
  13. 20 Jun, 2021 3 commits
  14. 17 Jun, 2021 3 commits
    • Ryoko Noda's avatar
      Add info about ttype-assignment · 954775ec
      Ryoko Noda authored
      Added ttype-assignment.ipynb to the instructions and list of borrowed files.
      954775ec
    • Ryoko's avatar
      Ran ttype-assignment · 94c55074
      Ryoko authored
      Ran the last notebook for preprocessing, ttype-assignment.ipynb. This creates multiple images in the figures directory. It also saves a pickle file that is not tracked in this repo.
      
      I also created a figures directory so that ttype-assignment.ipynb can write images. This directory is not directly copied from the original work, and I just made it on the fly so the code can run.
      94c55074
    • Ryoko Noda's avatar
      Instructions about running patch-seq-data-load · 186545bb
      Ryoko Noda authored
      I forgot to add instructions about runnning patch-seq-data-load.ipynb so I added it.
      186545bb
  15. 15 Jun, 2021 2 commits
    • Ryoko Noda's avatar
      Added patch-seq-data-load.ipynb to borrowed files · 4fedf22d
      Ryoko Noda authored
      Added patch-seq-data-load.ipynb to the list of borrowed codes.
      4fedf22d
    • Ryoko's avatar
      Copied and ran patch-seq-data-load · 58c9fd0b
      Ryoko authored
      Ran patch-seq-data-load.ipynb from the original project. I didn't run into any problems with the filepaths and URLs this time, so the file is not modified from the original.
      
      This script generates one file, m1.pickle, but it is not tracked so it will not show up in the repo.
      58c9fd0b
  16. 14 Jun, 2021 8 commits
  17. 10 Jun, 2021 2 commits
  18. 08 Jun, 2021 2 commits