LIANA wrapper function
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"
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
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.
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))
#> Expression from the `RNA` assay will be used
#> Running LIANA with `seurat_annotations` as labels!
#> Warning: 3465 genes and/or 0 cells were removed as they had no counts!
#> LIANA: LR summary stats calculated!
#> Now Running: Cellphonedb
#> Now Running: Sca