View source: R/interaction_graph.R
GenerateCCIM | R Documentation |
Calculate cell-cell interaction matrix
GenerateCCIM(
object,
assay = "SCT",
slot = "data",
species = "human",
database = "OmniPath",
ligands = NULL,
recepts = NULL,
senders = NULL,
receivers = NULL,
weighted = F,
nichenet_results = NULL,
pearson.cutoff = 0.075,
scale.factors = c(1.5, 3),
weight.method = "sum"
)
object |
A seurat object |
assay |
Assay in Seurat object from which to pull expression values |
slot |
Slot within assay from which to pull expression values |
species |
character. Name of species from which to load ligand-receptor databases. One of: "human", "mouse", "rat". Default: "human" |
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. |
senders |
Character vector of cell names to be used as sender cells for interaction graph generation. By default, all cells in object are used as senders. |
receivers |
Character vector of cell naems to be used as receiver cells for interaction graph generation. By default, all cells in object are used as receivers. |
weighted |
logical. Weight the cell-cell interaction graph by ligands predicted to be active by NicheNet? Default: FALSE |
nichenet_results |
List or matrix. Predicted ligand activities using Scriabin's implementation of NicheNet in RankActiveLigands |
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). |
weight.method |
One of "sum" or "product". Method to use for weighting CCIM by ligand activities. "Sum" sums receptor expression values with ligand activities passing the |
Returns a Seurat object with assay "CCIM" where columns are cell-cell pairs and rows are ligand-receptor pairs. "Expression" values are the geometric mean expression value between each pair of sender and receiver cells. By default, names ligand-receptor pairs and cell-cell pairs are separated by "="
Browaeys, et al. Nature Methods (2019)
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