BuildWeightedInteraction | R Documentation |
Build summarized interaction graph weighted by predicted ligand activities
BuildWeightedInteraction(
object,
nichenet_results,
assay = "SCT",
slot = "data",
pearson.cutoff = 0.075,
scale.factors = c(1.5, 3),
species = "human",
database = "OmniPath",
ligands = NULL,
recepts = NULL,
correct.depth = T,
graph_name = "weighted_interaction"
)
object |
A Seurat object |
nichenet_results |
List or matrix. Predicted ligand activities using Scriabin's implementation of NicheNet in RankActiveLigands |
assay |
Assay in Seurat object from which to pull expression values |
slot |
Slot within assay from which to pull expression values |
pearson.cutoff |
numeric. Threshold for determining which ligand activities are "active". Ligands below this threshold will be considered inactive and not used for weighting. Default: 0.075 |
scale.factors |
numeric. Determines the magnitude of ligand and receptor expression values weighting by their predicted activities. Given scale factors of c(x,y), ligand-receptor pairs where the ligand's pearson = pearson.cutoff will be weighted by a factor of x, and the ligand with the highest pearson will be weighted by a factor of y. Default: c(1.5,3). |
species |
Name of species for which to pull ligand-receptor interactions. One of "human", "mouse", or "rat" |
database |
Name of ligand-receptor database to use. Default: "OmniPath" When species is "human", one of: OmniPath, CellChatDB, CellPhoneDB, Ramilowski2015, Baccin2019, LRdb, Kirouac2010, ICELLNET, iTALK, EMBRACE, HPMR, Guide2Pharma, connectomeDB2020, talklr, CellTalkDB When species is "mouse" or "rat", only "OmniPath" is supported. To pass a custom ligand-receptor database to this function, set database = "custom" |
ligands |
Character vector of custom ligands to use for interaction graph generation. Ignored unless database = "custom" When ligands is supplied, recepts must also be supplied and equidimensional. |
recepts |
Character vector of custom receptors to use for interaction graph generation. Ignored unless database = "custom" When recepts is supplied, ligands must also be supplied and equidimensional. |
correct.depth |
Correct summarized interaction graph for sequencing depth by linear regression. The sequencing depth of a cell-cell pair is the sum of UMI counts for each cell |
graph_name |
Name of summarized interaction graph to place into output. Default "weighted_interaction" |
ranked_genes |
Cell-resolved gene signatures, used only when specific = T |
Returns a Seurat object with a weighted summarized interaction graph in the Graphs slot
Browaeys, et al. Nature Methods (2019)
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