A useful function to tile the point within certain cells when loading map, in order to achieve a faster, more comfortable experience.

python3 -m http.server

Run above code in cellTile directory to start a http server. Then in any explorer, go into:

http://localhost:8000/

and open your .html file.

• image_tiles/
  • Output from Tileup, used as the image layer of map;
• roi.pos0.all.cells.converted.txt
  • Draw the boundary of cells, also used to generate the cell_centroid.csv
• cell_centroid.csv
  • A csv file with 3 columns: cell ID, x coordinate, y coordinate
  • Give location information of cell centroids
  • Generated by get_centroid.py
• Pos0_647nm_561nm_combined_clean.csv
  • File contains location and cell information of each single transcription.
  • First column as the x coord; Second as the y coord;
  • Fourth as cell id; Fifth as gene ID
• gene.list
  • A single-column file with each row as a gene ID
  • Used in the dropdown box when doing selecting genes functions.
• js/script.js
  • Need to change the parameters to fit your own data
    • Map size should fit with your location information (axis, coordinate, ...)
    • Stain image layers to choose
    • Change file names in every fetch functions into your corresponding file names
• cells/
  • A collection of csv files each containing all data for each single cell. Names as the cell IDs.
  • Geenrated by pre_processing.R

• Old version which load the whole data at once; may not be compatible when data is really large; still can work in small dataset.
• Also can work. If interested, please give a try.