Package index • liana

Main Functions

Core LIANA workflow functions

liana_wrap(): LIANA wrapper function

liana_aggregate(): Function to Aggregate CCC Method Results

liana_prep(): Function to handle different types of object as input and do basic quality checks

liana_pipe(): Liana Pipe which runs DE analysis and merges needed information for LR inference

Visualization

Plotting functions

liana_dotplot(): Liana dotplot interactions by source and target cells

liana_heatmap(): Communication by cell type Heatmap

heat_freq(): Communication Frequency heatmap plot

chord_freq(): Frequency ChordDiagram

Score Calculation

Internal scoring functions

get_c2c_factors(): Returns tensor cell2cell results

get_connectome(): Function to obtain connectome-like weights

get_curated_omni(): Function to Generate the Curated (Default) LIANA resource

get_logfc(): Function to obtain logFC weights

get_lr_resources(): Helper function that returns the name of each intercell resource in OmniPath

get_natmi(): Function to obtain NATMI-like weights

get_partners(): Retrieves intercellular communication partners (ligands or receptors) from one ligand-receptor resource.

get_permutations(): Helper Function to generate shuffled means

get_sca(): Function to obtain SingleCellSignalR-like scores

liana_call(): Wrapper Function to obtain scores via liana_pipe

liana_scores(): Function to obtain different scoring schemes

Tensor Decomposition

Multi-sample analysis with cell2cell

liana_tensor_c2c(): Wrapper function to run `cell2cell_tensor` with LIANA output.

decompose_tensor(): Wrapper function to run `cell2cell_tensor` decomposition on a prebuilt tensor.

get_c2c_factors(): Returns tensor cell2cell results

plot_c2c_overview(): Function to plot an Overview of tensor-c2c results

plot_context_boxplot(): Generate boxplots with significance

plot_context_heat(): Plot a Heatmap of context loadings

plot_lr_heatmap(): Function to plot a UMAP of context loadings

plot_c2c_cells(): Plot the product of loadings between the source and target loadings within a factor

preprocess_scores(): Helper function to deal with tensor sparsity and liana's scores as in Python

generate_lr_geneset(): Generate a geneset resource for each LR

Resources & Methods

Access available resources and methods

show_resources(): Helper Function to return the Resources in LIANA

show_methods(): Helper Function to return the methods in LIANA

select_resource(): Helper Function to Handle resource choices

liana_defaults(): Function to pass Default Arguments for each method

Utilities

Helper functions

decomplexify(): Helper Function to 'decomplexify' ligands and receptors into individual subunits

recomplexify(): Helper function to account for complexes in the resources

generate_homologs(): Function to generate a homologous OmniPath resource

generate_orthologs(): Deprecated call to generate_homologs

show_homologene(): Helper function to show available organisms via OmnipathR's homologene resource

minmax(): Helper min-max normalization function

min0(): Helper Function which returns the value closest to 0

mean0(): Helper Function which returns the mean, unless there is a 0 value then it returns 0

rank_method(): Helper function to rank each method

rank_aggregate(): Aggregate CCC Method results and by both magnitude and specificity ranks

filter_nonabundant_celltypes(): Filter nun-abundant cell types

assign_lr_weights(): Helper function to assign weights

liana_bysample(): Wrapper around `liana_wrap` to run liana for each sample.

liana_message(): LIANA message/warning helper function to allow for verbosity

External Methods (Deprecated)

Original method pipelines

call_cellchat(): Run CellChat with OmniPath function [[DEPRECATED]]

call_connectome(): Function to call connectome with databases from OmniPath [[DEPRECATED]]

call_italk(): Run iTALK with OmniPath data [[DEPRECATED]]

call_natmi(): Call NATMI Pipeline from R with Resources Querried from OmniPath [[DEPRECATED]]

call_sca(): Function to call SingleCellSignalR with databases from OmniPath [[DEPRECATED]]

call_squidpy(): Call Squidpy Pipeline via reticulate with OmniPath and format results

FormatConnectome(): Helper function to filter and format connectome

FormatNatmi(): Load NATMI results from folder and format appropriately

FormatSCA(): Helper function to format SingleCellSignalR results

FormatiTALK(): Helper Function to Filter and format iTalk results