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.

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.