Phenotrax

Phenotrax generates an idealized trajectory between two cellular populations and positions additional cells with respect to said trajectory

Inputs:

• NA - matrix with cells corresponding to the 0 state subpopulation (initial phenotype). rows correspond to each cell in the subpopulation and columns correspond to each parameters that has been measured for each cell
• A - matrix with cells corresponding to the 1 state subpopulation (final phenotype). rows correspond to each cell in the subpopulation and columns correspond to each parameters that has been measured for each cell
• D - matrix with cells corresponding to additional, previosuly unseen cells. rows correspond to each cell in the subpopulation and columns correspond to each parameters that has been measured for each cell

Outputs:

• X_positions - relative position of each cell with respect to the idealized trajecotry created between the 0 and 1 state. Rows correspond to each cell input in matrix D. The 2 columns correspond to (t) relative position of the cell along the idealized trajectory; (d) minimal distance of the cell to the idealized trajectory.
• Also a 'results.txt' file is generated with the X_positions matrix