View source: R/AntibodyForests_communities.R
AntibodyForests_communities | R Documentation |
Performs community detection/clustering on the AntibodyForests sequence similarity networks. Annotates the resulting networks with a new igraph vertex attribute ('community') for downstream analysis or plotting. Can also add these annotations back to the VGM.
AntibodyForests_communities( trees, VGM, community.algorithm, graph.type, which.bipartite, features, count.level, additional.parameters )
trees |
AntibodyForests object/list of AntibodyForests objects - the resulting sequence similarity or minimum spanning tree networks from the AntibodyForests function |
VGM |
VGM object - for annotating the VGM object with the resulting clusters/communities. |
community.algorithm |
string - denotes the community/clustering algorithm to be used. Several options are available: 'louvain', 'walktrap', 'edge_betweenness', 'fast_greedy', 'label_prop', 'leading_eigen', 'optimal', 'spinglass'. |
graph.type |
string - the graph type available in the AntibodyForests object which will be used as the function input. Currently supported network/analysis types: 'tree' (for the minimum spanning trees or sequence similarity networks obtained from the main AntibodyForests function), 'heterogeneous' for the bipartite graphs obtained via AntibodyForests_heterogeneous, 'dynamic' for the dynamic networks obtained from AntibodyForests_dynamics. |
which.bipartite |
string - whether to perform clustering on the cell layer of the bipartite/heterogeneous graph ('cells'), sequence layer ('sequences') or on both ('both'). |
features |
vector of strings - features to be considered in the output bar plots (of feature counts per cluster). These features must be integrated when creating the initial AntibodyForests objects by using the node.features parameter. |
count.level |
string - whether to consider cells ('cells') or sequences ('sequences') when counting the unique feature values in the output bar plots. When counting by sequences/nodes, each unique node is assigned the feature value of the majority of its consituent cells. |
additional.parameters |
named list - additional parameters to be considered in the clustering algorithm, as mentioned in the igraph documentation for the respective algorithms (e.g., additional.parameters = list(resolution = 0.25)). |
a single AntibodyForests object or a nested list of AntibodyForests objects (depending on the input type) with community/cluster annotations as a vertex attribute. Additional bar plots of feature counts per resulting cluster are also displayed.
AntibodyForests, AntibodyForests_plot
## Not run: AntibodyForests_communities(trees = AntibodyForests_object, VGM = NULL, community.algorithm = 'louvain', graph.type = 'tree', features = 'seurat_clusters', count.level = 'cells', additional.parameters = list(resolution = 0.25)) ## End(Not run)
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