liana_defaults: Function to pass Default Arguments for each method

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

Function to pass Default Arguments for each method

Description

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

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.

Value

A list of the default parameters for each method

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'))

saezlab/liana documentation built on Aug. 10, 2024, 8:14 a.m.