Tools

The tl module contains a collection of useful tools to use during analysis.

tl.mfi	Calculates the median/mean fluorescence intensities (MFI).
tl.fop	Calculates the frequency of parents.
tl.gate_frequencies	Calculates the gate frequencies as a percentage.
tl.gate_frequencies_mem	Calculates the gate frequencies as a percentage.
tl.umap	Calculates UMAP embedding.
tl._compute_umap	Internal function to compute the UMAP embedding.
tl.tsne	Calculates TSNE embedding.
tl._compute_tsne	Internal function to compute the TSNE embedding.
tl.diffmap	Diffusion Map Embedding calculation
tl._compute_diffmap	Internal function to compute the Diffmap embedding.
tl.pca	Principal component analysis
tl._compute_pca	Internal function to compute the PCA embedding.
tl.parc	Computes PARC clustering.
tl.flowsom	Computes FlowSOM clustering.
tl.leiden	Computes Leiden clustering.
tl.phenograph	Computes PhenoGraph clustering.
tl.neighbors	Computes Neighbors.
tl.pca_samplewise	Computes samplewise PCA based on either the median fluorescence values (MFI) or frequency of parent values (FOP).
tl.tsne_samplewise	Computes samplewise TSNE based on either the median fluorescence values (MFI) or frequency of parent values (FOP).
tl.mds_samplewise	Computes samplewise MDS based on either the median fluorescence values (MFI) or frequency of parent values (FOP).
tl.umap_samplewise	Computes samplewise UMPA based on either the median fluorescence values (MFI) or frequency of parent values (FOP).
tl.correct_expression	Function to correct the expression values based on a joint PCA embedding.
tl.harmony_integrate	Computes harmony integration.
tl.scanorama_integrate	Computes scanorama integration.