Function to pass Default Arguments for each method

Usage

liana_defaults(
  assay = "RNA",
  assay.type = "logcounts",
  expr_prop = 0.1,
  seed = 1004,
  complex_policy = "mean0",
  parallelize = FALSE,
  workers = 8,
  permutation.params = NULL,
  liana_pipe.params = NULL,
  liana_call.params = NULL,
  cellphonedb.params = NULL,
  natmi.params = NULL,
  sca.params = NULL,
  connectome.params = NULL,
  cytotalk.params = NULL,
  logfc.params = NULL,
  cellchat.params = NULL,
  squidpy.params = NULL,
  call_sca.params = NULL,
  call_natmi.params = NULL,
  call_connectome.params = NULL,
  call_italk.params = NULL,
  ...
)

Arguments

assay: Assay name passed to `call_italk`, `call_sca`, `call_cellchat`, and `call_connectome`
assay.type: - the type of data to be used to calculate the means (logcounts by default), available options are: "counts" and "logcounts"
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.
seed: random seed integer
complex_policy: policy how to account for the presence of complexes.
parallelize: whether to parallelize cellphonedb-like
workers: number of workers to be called
permutation.params: list of parameters passed to permutation methods
liana_pipe.params: list of Parameters passed to NATMI liana_pipe
liana_call.params: list of Parameters passed to NATMI liana_call
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
cellchat.params: list of Parameters passed to CellChat call_cellchat
squidpy.params: list of Parameters passed to Squidpy call_squidpy
call_sca.params: list of Parameters passed to SingleCellSignalR call_sca
call_natmi.params: list of Parameters passed to NATMI call_natmi
call_connectome.params: list of Parameters passed to Connectome call_connectome
call_italk.params: list of Parameters passed to iTALK call_italk

Value

A list of the default parameters for each method

Details

The default parameters for each method can also be overwritten by manually passing a list of parameters for the appropraite method liana_wrap

Further, each `get_*` method will by default obtain the default params passed via liana_pipe and liana_call. This is done so that most steps required for the calculation of these methods are undertaken only once.

NB! LIANA's internal methods are made consistent. There is no reason to pass specific parameters to any of them. Thus, it is best that one sticks to the non-nested parameters of this function (i.e. excluding `.params`), unless a very specific reason requires any of LIANA's internal parameters to be changed.

Examples

liana_path <- system.file(package = "liana")
# load testdata
testdata <- readRDS(file.path(liana_path , "testdata", "input", "testdata.rds"))
# get a `named` list with all default parameters passed to liana.
def_params <- liana_defaults()
# any of these can then be overwritten and passed to `...` in `liana_wrap`
# with the `.params` suffix to the parameter name type. For example,
liana_res <- liana_wrap(testdata,
                        permutation.params = list(nperms=2),
                        liana_pipe.params = list(test.type='wilcox'))
#> 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: Natmi
#> Now Running: Connectome
#> Now Running: Logfc
#> Now Running: Sca
#> Now Running: Cellphonedb