Digital Lineage Tracing¶
workflow¶
Step 01¶
for each pair of time points,
calculate the similarity array for each pair of cells between those two datasets
save the closest cell in another dataset for every cell.
Usage :
python3 s01.CellCor.py <-i in.lst> [-o output folder, default ./]
example of in.lst¶
time0
time1
time2
time3
and we will load time0.h5ad, time1.h5ad, time2.h5ad, time3.h5ad.
Step 02¶
for each pair of time points, calculate the mapping number of cells for all clusters.
Usage:
python3 s02.get_number_anno.py <-i in.lst> [-o output folder, default ./]
we will load time0.h5ad, time1.h5ad, time2.h5ad, time3.h5ad. and data generated by s01 in output folder!
Step 03¶
filter weak connections.
Usage:
python3 s02.filter.py [-f filter threshold, default 0.05] [-o output folder, default ./]
we will load data generated by s02 in output folder!
Step 04¶
plot the final sankey plot.