liana_wrap: LIANA wrapper function

In saezlab/ligrec_decoupler: LIANA: a LIgand-receptor ANalysis frAmework

LIANA wrapper function

Description

LIANA wrapper function

Usage

liana_wrap(
  sce,
  method = c("natmi", "connectome", "logfc", "sca", "cellphonedb"),
  resource = c("Consensus"),
  idents_col = NULL,
  external_resource,
  min_cells = 5,
  return_all = FALSE,
  supp_columns = NULL,
  verbose = TRUE,
  assay = NULL,
  .simplify = TRUE,
  cell.adj = NULL,
  base = NULL,
  ...
)

Arguments

sce	'SingleCellExperiment' object or 'SeuratObject'
method	method(s) to be run via liana
resource	resource(s) to be used by the methods ('Consensus' by default), Use 'all' to run all 'human' resources in one go), or 'custom' to run liana_wrap with an appropriately formatted custom resource, passed via 'exernal_resource'
idents_col	the cell identities/labels to be used. By default set to NULL, and will used the active Idents or colLabels from the seurat_object or SCE, respectively.
external_resource	external resource in OmniPath tibble format
min_cells	minimum cell per cell identity to be considered for analysis
return_all	whether to return all possible interactions. Any interaction with 'expr_prop' below the specific threshold will be assigned to the *worst* possible score in those that pass the threshold. For example, p-values from CellPhoneDB will be assigned to max(pvalue) - likely 1, and lr_means will be assigned to min(lr_means). Note that this applies only to the internal methods of liana.
supp_columns	any supplementary/additional columns which are to be returned by liana. Possibilities include: c("ligand.expr", "receptor.expr" "ligand.stat", "receptor.stat", "ligand.pval", "receptor.pval", "ligand.FDR", "receptor.FDR", etc)
verbose	logical whether to output messages and warnings ('TRUE' by default)
assay	assay to be used by Seurat, by default set to 'NULL' and will use the DefaultAssay.
.simplify	if methods are run with only 1 resource, return a list of tibbles for each method (default), rather than a list of lists with method-resource combinations
cell.adj	cell adjacency tibble/dataframe /w weights by which we will 'multiply' the relevant columns. Any cell pairs with a weights of 0 will be filtered out. Note that if working with LIANA's default methods, we suggest weights >= 0 & =< 1. This ensure that all methods' score will be meaningfully weighed without changing the interpretation of their scores, thus allow one to filter SCA, rank NATMI, etc.
base	Default to NULL (i.e. log2-transformation is assumed for SCE, and log-tranformation for Seurat). This is a requred step for the calculation of the logFC method - ensures that any other preprocessing of the counts is preserved. One could also pass 'NaN' if they wish to use the counts stored in the counts assay/slot, or any other number according to the base that was used for log-tranformation.
...	Arguments passed on to liana_defaults expr_prop minimum proportion of gene expression per cell type (0.1 by default). Note that when working with complexes, the minimum subunit proportion will be used for filtering. complex_policy policy how to account for the presence of complexes. seed random seed integer parallelize whether to parallelize cellphonedb-like workers number of workers to be called liana_pipe.params list of Parameters passed to NATMI liana_pipe liana_call.params list of Parameters passed to NATMI liana_call cellchat.params list of Parameters passed to CellChat call_cellchat squidpy.params list of Parameters passed to Squidpy call_squidpy call_connectome.params list of Parameters passed to Connectome call_connectome call_italk.params list of Parameters passed to iTALK call_italk call_natmi.params list of Parameters passed to NATMI call_natmi call_sca.params list of Parameters passed to SingleCellSignalR call_sca cellphonedb.params list of Parameters passed to liana's internal cellphonedb implementation cellphonedb_score natmi.params list of Parameters passed to liana's internal edge_specificity implementation natmi_score sca.params list of Parameters passed to liana's internal LRScore implementation sca_score connectome.params list of Parameters passed to liana's internal connectome's weight_sc implementation connectome_score cytotalk.params list of Parameters passed to liana's internal crosstalk scores implementation cytotalk_score logfc.params list of Parameters passed to liana's internal logFC implementation logfc_score permutation.params list of parameters passed to permutation methods assay.type - the type of data to be used to calculate the means (logcounts by default), available options are: "counts" and "logcounts"

Details

LIANA wrapper method that can be used to call each method with a given set of intercellular resources from the OmniPath universe. Please see 'liana_defaults()' for more information about the default parameters passed used by 'liana_wrap', if you wish to modify them.

Value

A list of method-resource results - i.e. provided resources are run with each method If only one resource is selected, a single tibble (with results for that resource) will be returned for each of the selected methods

Examples

liana_path <- system.file(package = "liana")
# load testdata
testdata <- readRDS(file.path(liana_path , "testdata", "input", "testdata.rds"))
# run only 2 methods from liana
liana_res <- liana_wrap(testdata, method = c('cellphonedb', 'sca'),
                        resource = 'Consensus', # default resource
                        # example run with *only* 2 permutations for cpdb
                        permutation.params = list(nperms = 2))

saezlab/ligrec_decoupler documentation built on Aug. 10, 2024, 8:56 a.m.