View source: R/AntibodyForests_node_transitions.R
AntibodyForests_node_transitions | R Documentation |
Node transitions represent the number of (un)directed edges between two feature values of a given feature type in a single sequence similarity network or minimum spanning trees (e.g., between VDJ_cgene = 'IGHA' and VDJ_cgene = 'IGHM'). The resulting AntibodyForests objects will contain a new slot - node_transitions. Will also output bar plots of the transition frequencies.
AntibodyForests_node_transitions( trees, features, combined, graph.type, permutation.test, exclude.germline, exclude.intermediates, n.permutations, plot.results, parallel )
trees |
nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function. |
features |
vector of strings - features for the node transition counting. Each node will be assigned the dominant feature if its constituent cells have different feature values (e.g., for features = c('seurat_clusters')). These features need to be first added as vertex attributes when creating the AntibodyForests networks, specified in the node.features parameter of AntibodyForests. |
combined |
boolean - if T, will assign a new feature by combining the feature values as specified in the features parameter (e.g., if node 1 has VDJ_cgene = 'IGHM' and seurat_clusters = 1, will create a new feature = 'IGHM 1' for that node, for joint node transitions). |
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. |
permutation.test |
boolean - if T, will perform a permutation statistical test on the node feature transition values. |
exclude.germline |
boolean - if T, will exclude the germline from the node feature transitions counting. |
exclude.intermediates |
boolean - if T, will exclude the intermediate nodes expanded using AntibodyForests_expand_intermediates() from the node transitions counting. |
n.permutations |
integer - number of node feature permutations for the permutation test. |
plot.results |
boolean - if T, will display the node transitions counts as bar plots, per feature specified in the features parameter. |
parallel |
boolean - whether to execute the main subroutine in parallel or not. Requires the 'parallel' R package to be installed. |
nested list of AntibodyForests objects for each clonotype and each sample or single object, with an additional node_transitions slot of transition/edge counts.
## Not run: AntibodyForests_node_transitions(trees, graph.type = 'tree', features = 'VDJ_cgene', plot.results = T) ## End(Not run)
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