# Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation

## Documentation for package ‘CytOpT’ version 0.9.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

barplot_prop | Function to display a bland plot in order to visually assess the agreement between CytOpt estimation of the class proportions and the estimate of the class proportions provided through manual gating.
Bland_Altman | Bland & Altman plot
CytOpT | Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function the computation of the estimate of the class proportions is done with a descent ascent or minmax or two algorithms.
cytopt_desasc_r | Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function the computation of the estimate of the class proportions is done with a descent ascent algorithm.
cytopt_minmax_r | Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function an additional regularization parameter on the class proportions enables a faster computation of the estimator.
HIPC_Stanford | HIPC_Stanford data
HIPC_Stanford_1228_1A | HIPC_Stanford data
HIPC_Stanford_1228_1A_labels | HIPC_Stanford data
HIPC_Stanford_1369_1A | HIPC_Stanford data
HIPC_Stanford_1369_1A_labels | HIPC_Stanford data
KL_plot | Kullback-Leibler divergence plot
Label_Prop_sto_r | Computes a classification on the target data
plot.CytOpt | CytOpt plot
print.CytOpt | CytOpt print
print.summary.CytOpt | CytOpt print summary
summary.CytOpt | CytOpt summary