cellTile

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

How to start

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.

Necessary input files

• image_tiles/

  • output from Tileup, used as the image of map;

• roi.pos0.all.cells.converted.txt

  • draw the boundary of cells, also used to generate the centroid by get_centroid.py

• Pos0_647nm_561nm_combined_clean.csv

  • file contains location and cell information of each single transcription.
  • First col as the x coord; Second as the y coord;
  • Fourth as cell id; Fifth as gene ID

• gene.list

  • A single-col file with every gene ID as a single row
  • Used in the dropdown box

• js/script.js

  • Need to change the parameters to fit your own data
    • Map size should fit with your location information (axis, coordinate, ...)
    • Stain layers to choose
    • Colorlist now have about 150 colors; would report error if there are more cells. Can manually add new color to prevent.

• cells/

  • A collection of csv files each containing all data for each single cell. Names as the cell IDs. Geenrated by pre_processing.R.

About archive

• 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.