View source: R/AntibodyForests_heterogeneous.R
AntibodyForests_heterogeneous | R Documentation |
Creates a bipartite network from a Seurat object and an already inferred AntibodyForests sequence similarity/ minimum spanning tree network.
AntibodyForests_heterogeneous( trees, GEX.object, node.features, cell.graph.type, recluster.cells, recluster.resolution, snn.threshold, keep.largest.cc, parallel )
trees |
AntibodyForests object/list of AntibodyForests objects - the resulting sequence similarity or minimum spanning tree networks from the AntibodyForests function. |
GEX.object |
Seurat object/ VGM[[2]] for the inferred AntibodyForests networks (must include all cells available in the AntibodyForests object). |
node.features |
vector of strings - gene names in the Seurat object to be added as igraph vertex attributes in the resulting heterogeneous networks (will add gene expression per gene). |
cell.graph.type |
string - graph algorithm for building the cell-cell/ nearest-neighbour graphs, as done by the Seurat::FindNeighbors() function. 'knn' for the K nearest-neighbour graphs, 'snn' for the shared nearest-neighbour graphs. |
recluster.cells |
boolean - whether to recluster the resulting cell graphs or keep the already existing Seurat cluster definitions. |
recluster.resolution |
numeric - recluster resolution for the Louvain algorithm if recluster.cells is TRUE. |
snn.threshold |
numeric - SNN edge weight threshold to further prune edges in the cell graphs (increased value = sparser cell graphs). Defaults to 1/15 (as done in the Seurat::FindNeighbors function). |
keep.largest.cc |
boolean - whether to keep only the largest connected component in the cell graphs or keep all singletons/doubletons/etc., as well. |
parallel |
boolean - whether to execute the heterogeneous graph building algorithm in parallel or not. Requires the 'parallel' R package. |
nested list of AntibodyForests objects for each clonotype and each sample/timepoint or a single AntibodyForests object, with a new added object slot for the heterogeneous graph.
## Not run: AntibodyForests_heterogeneous(trees, GEX.object = VGM[[2]], cell.graph.type = 'snn') ## End(Not run)
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