wot provides a command line interface that offers fine-grained control over calculations.
Help is available for each tool using the syntax wot tool -h. For example, wot optimal_transport -h.


convert_matrix

Parameter Description
matrix File to convert
format Output file format
Choices: gct, h5ad, loom, txt
out Output file name
obs Row metadata to join with ids in matrix
var Column metadata to join with ids in matrix
transpose Transpose the matrix before saving
Example Usage:
wot convert_matrix my_matrix.h5ad --format txt
This command converts my_matrix.h5ad to txt format.

cells_by_gene_set

Parameter Description
score Gene sets scores generated from the gene_set_scores command
filter Comma separated list of column names to include
quantile Quantile for cells to be considered a member of a cell set
Default: 99
out Output file name prefix
Default: wot

census

Parameter Description
tmap Directory of transport maps as produced by optimal transport
cell_set gmt, gmx, or grp file of cell sets.
day The starting timepoint at which to consider the cell sets
out Output files prefix
Default: census

diff_exp

Parameter Description
matrix A matrix with cells on rows and features, such as genes or pathways on columns
fate Fate dataset produced by the fate tool
cell_days File with headers "id" and "day" corresponding to cell id and days
nperm Number of permutations
smooth_p_values Smooth p-values
fold_change Limit permutations to genes which show at least X-fold difference (log-scale) between the two groups of cells
Default: 0.25
cell_days_field Field name in cell_days file that contains cell days
Default: day
cell_day_filter Comma separated list of days to include (e.g. 12,14,16)
gene_filter File with one gene id per line
verbose Print progress
Example Usage:
wot diff_exp --matrix data/ExprMatrix.h5ad --cell_days data/cell_days.txt --fate IPS_d17_fates.txt --fold_change 0 --gene_filter data/TFs.txt --cell_day_filter 14 --verbose
This command computes differentially expressed genes at day 14 that are predictive of IPS fate at day 17.

fates

Parameter Description
tmap Directory of transport maps as produced by optimal transport
cell_set gmt, gmx, or grp file of cell sets.
day Day to consider for cell sets
cell_set_filter Comma separated list of cell sets to include (e.g. IPS,Stromal)
format Output matrix file format
Default: txt
embedding Optional file with id, x, y used for plotting
out Prefix for output file names
Default: wot
verbose Print cell set information
Example Usage:
wot fates --tmap tmaps/serum --cell_set data/major_cell_sets.gmt --day 17 --cell_set_filter IPS --out IPS_d17 --verbose
This command computes IPS cell fates.

gene_set_scores

Parameter Description
matrix A matrix with cells on rows and genes on columns
gene_sets Gene sets in gmx, gmt, or grp format
method Method to compute gene set scores
Choices: mean_z_score, mean, mean_rank
Default: mean_z_score
cell_filter File with one cell id per line to include
gene_set_filter Gene sets to include
max_z_score Threshold z-scores at specified value
Default: 5
nperm Number of permutations to perform
out Output file name prefix
Default:
transpose Transpose the matrix
format Output file format
Choices: gct, h5ad, loom, txt
Default: txt
verbose Print verbose information
Example Usage:
wot gene_set_scores --matrix data/ExprMatrix.h5ad --method mean_z_score --gene_sets data/gene_sets.gmx
This command computes gene set scores. See notebooks for an example of converting gene set scores to growth rates.

neighborhood_graph

Parameter Description
matrix A matrix with cells on rows and features, such as genes or pathways on columns
gene_filter File with one gene id per line to include from the matrix
cell_filter File with one cell id per line to include from the matrix
transpose Transpose the matrix
pca_comps Number of PCA components.
Default: 50
diff_comps Number of diffusion components.
Default: 15
neighbors Number of nearest neighbors
Default: 15
space Space to compute the neighborhood graph in
Choices: dmap, pca, input
out Output file name. The file is saved in gexf format (https://gephi.org/gexf/format/)

optimal_transport

Parameter Description
matrix A matrix with cells on rows and features, such as genes or pathways on columns
cell_days File with headers "id" and "day" corresponding to cell id and days
cell_growth_rates File with "id" and "cell_growth_rate"headers corresponding to cell id and growth rate per day.
parameters Optional two column parameter file containing parameter name and value
config Configuration per timepoint or pair of timepoints
transpose Transpose the matrix
local_pca Convert day pairs matrix to local PCA coordinates.Set to 0 to disable
Default: 30
growth_iters Number of growth iterations for learning the growth rate.
Default: 1
gene_filter File with one gene id per line to use for computingcost matrices (e.g. variable genes)
cell_filter File with one cell id per line to include
cell_day_filter Comma separated list of days to include (e.g. 12,14,16)
scaling_iter Number of scaling iterations for OT solver
Default: 3000
inner_iter_max For OT solver
Default: 50
epsilon Controls the entropy of the transport map. An extremely large entropy parameter will give a maximally entropic transport map, and an extremely small entropy parameter will give a nearly deterministic transport map (but could also lead to numerical instability in the algorithm
Default: 0.05
lambda1 Regularization parameter that controls the fidelity of the constraints on p
Default: 1
lambda2 Regularization parameter that controls the fidelity of the constraints on q
Default: 50
max_iter Maximum number of scaling iterations. Abort if convergence was not reached
Default: 10000000.0
batch_size Number of scaling iterations to perform between duality gap check
Default: 5
tolerance Maximal acceptable ratio between the duality gap and the primal objective value
Default: 1e-08
epsilon0 Warm starting value for epsilon
Default: 1
tau For OT solver
Default: 10000
ncells Number of cells to downsample from each timepoint and covariate
ncounts Sample ncounts from each cell
solver The solver to use to compute transport matrices
Choices: duality_gap, fixed_iters
Default: duality_gap
cell_days_field Field name in cell_days file that contains cell days
Default: day
cell_growth_rates_field Field name in cell_growth_rates file that contains growth rates
Default: cell_growth_rate
verbose Print progress information
format Output file format
Choices: h5ad, loom
Default: h5ad
no_overwrite Do not overwrite existing transport maps if they exist
out Prefix for output file names
Default: ./tmaps
Example Usage:
wot optimal_transport --matrix data/ExprMatrix.var.genes.h5ad --cell_days data/cell_days.txt --cell_filter data/serum_cell_ids.txt --growth_iters 3 --cell_growth_rates data/growth_gs_init.txt --out tmaps/serum --verbose
This command computes transport maps for all consecutive time points.

optimal_transport_validation

Parameter Description
matrix A matrix with cells on rows and features, such as genes or pathways on columns
cell_days File with headers "id" and "day" corresponding to cell id and days
cell_growth_rates File with "id" and "cell_growth_rate"headers corresponding to cell id and growth rate per day.
parameters Optional two column parameter file containing parameter name and value
config Configuration per timepoint or pair of timepoints
transpose Transpose the matrix
local_pca Convert day pairs matrix to local PCA coordinates.Set to 0 to disable
Default: 30
growth_iters Number of growth iterations for learning the growth rate.
Default: 1
gene_filter File with one gene id per line to use for computingcost matrices (e.g. variable genes)
cell_filter File with one cell id per line to include
cell_day_filter Comma separated list of days to include (e.g. 12,14,16)
scaling_iter Number of scaling iterations for OT solver
Default: 3000
inner_iter_max For OT solver
Default: 50
epsilon Controls the entropy of the transport map. An extremely large entropy parameter will give a maximally entropic transport map, and an extremely small entropy parameter will give a nearly deterministic transport map (but could also lead to numerical instability in the algorithm
Default: 0.05
lambda1 Regularization parameter that controls the fidelity of the constraints on p
Default: 1
lambda2 Regularization parameter that controls the fidelity of the constraints on q
Default: 50
max_iter Maximum number of scaling iterations. Abort if convergence was not reached
Default: 10000000.0
batch_size Number of scaling iterations to perform between duality gap check
Default: 5
tolerance Maximal acceptable ratio between the duality gap and the primal objective value
Default: 1e-08
epsilon0 Warm starting value for epsilon
Default: 1
tau For OT solver
Default: 10000
ncells Number of cells to downsample from each timepoint and covariate
ncounts Sample ncounts from each cell
solver The solver to use to compute transport matrices
Choices: duality_gap, fixed_iters
Default: duality_gap
cell_days_field Field name in cell_days file that contains cell days
Default: day
cell_growth_rates_field Field name in cell_growth_rates file that contains growth rates
Default: cell_growth_rate
verbose Print progress information
covariate Covariate values for each cell
full_distances Compute full distances
day_triplets Three column file without a header containing start time, interpolation time, and end time
out Prefix for output file names
Default: tmaps_val
interp_size The number of cells in the interpolated population
Default: 10000
covariate_field Field name in covariate file that contains covariate
Default: covariate
Example Usage:
wot optimal_transport_validation --matrix data/ExprMatrix.var.genes.h5ad --cell_days data/cell_days.txt --cell_filter data/serum_cell_ids.txt --covariate data/batches.txt --cell_growth_rates tmaps/serum_g.txt --cell_growth_rates_field g2 --verbose
This command computes and plots optimal transport validation results.

trajectory

Parameter Description
tmap Directory of transport maps as produced by optimal transport
cell_set gmt, gmx, or grp file of cell sets.
day Day to consider for cell sets
cell_set_filter Comma separated list of cell sets to include (e.g. IPS,Stromal)
format Output matrix file format
Default: txt
embedding Optional file with id, x, y used for plotting
out Prefix for output file names
Default: wot
verbose Print cell set information
Example Usage:
wot trajectory --tmap tmaps/serum --cell_set data/major_cell_sets.gmt --day 18 --embedding data/fle_coords.txt --verbose
This command computes and plots trajectories using the serum transport maps and major cell sets.

trajectory_divergence

Parameter Description
matrix A matrix with cells on rows and features, such as genes or pathways on columns
cell_days File with headers "id" and "day" corresponding to cell id and days
distance_metric Distance metric (earth mover's distance or total variation)
Choices: emd, total_variation
Default: emd
trajectory One or more trajectory datasets as produced by the trajectory tool
compare If "match", compare trajectories with the same name. If "all", compare all pairs. If "within" compare within a trajectory. If a trajectory name, compare to the specified trajectory
Default: within
local_pca Convert day matrix to local PCA coordinates.Set to 0 to disable
Default: 30
plot Plot results
cell_filter File with one cell id per line to include
gene_filter File with one gene id per line to use for computingcost matrices (e.g. variable genes)
cell_day_filter Comma separated list of days to include (e.g. 12,14,16)
cell_days_field Field name in cell_days file that contains cell days
Default: day
out Prefix for output file names
Default: wot-trajectory
verbose Print progress
Example Usage:
wot trajectory_divergence --trajectory wot_trajectory.txt --cell_days data/cell_days.txt --matrix data/ExprMatrix.var.genes.h5ad --compare within --verbose --plot
This command computes the trajectory divergence.

trajectory_trends

transition_table

Parameter Description
tmap Directory of transport maps as produced by optimal transport
cell_set gmt, gmx, or grp file of cell sets.
start_time The start time for the cell sets to compute the transitions to cell sets at end_time
end_time The end time
out Prefix for ouput file.,
Default: wot
format Output file format
Choices: gct, h5ad, loom, txt
Default: h5ad