Build an undirected igraph graph from TCRdist() results

Builds an undirected igraph graph from the edges_df/nodes_df produced by TCRdist() (or cluster_tcrs(), which uses the same names). Every edge gets weight 1 regardless of its TCRdist value – i.e. this is a binary adjacency graph, not one weighted by TCRdist.

Usage

TCRdist_to_igraph(edges_df, nodes_df)

Arguments

edges_df

a data frame with columns "node1_idx" and "node2_idx" (1-indexed pairs of connected nodes), such as TCRdist()'s $edges_df. Any additional columns (e.g. "TCRdist") are kept as igraph edge attributes.

nodes_df

a data frame with one row per node and a "tcr_index" column giving each node's 1-indexed id (matching node1_idx/node2_idx), such as TCRdist()'s $nodes_df. Its other columns become igraph vertex attributes. Nodes with no edges are included in the graph as isolated vertices.

Value

an undirected igraph object with vcount() == nrow(nodes_df) and an edge attribute weight equal to 1 for every edge.

See also

TCRdist(), cluster_tcrs(), TCRdist_to_sparse_matrix()

Other tcr_similarity: TCRdist(), TCRdist_cpp(), TCRdist_old(), TCRdist_to_sparse_matrix(), add_to_tcr_network(), cluster_tcrs(), plot_clusters()

Examples

load_example_data(dataset = "SJTRC_minimal")
#> Example data already loaded into object: 'SJTRC_minimal'
df = get_all_tcrs(SJTRC_minimal, chain="paired", remove_duplicates = TRUE)
result = TCRdist(df, tcrdist_cutoff = 90)
#> Removed 384 TCRs with unknown V-segments (1.2%) from a total of 32,164 TCRs.
#> Removed 10 TCRs with short CDR3 segments (0.031%) from a total of 31,780 TCRs.
#> Removed 13,326 TCRs with non-functional CDR3 amino acid sequences (42%) from a total of 31,770 TCRs.
#> Filtered data frame contains 18,444 TCRs (57%) of original 32,164 TCRs.
#> ℹ Number of chunks: 190
#> ℹ 10% done — time taken so far: 0.25 seconds
#> ℹ 20% done — time taken so far: 0.5 seconds
#> ℹ 30% done — time taken so far: 0.74 seconds
#> ℹ 40% done — time taken so far: 0.98 seconds
#> ℹ 50% done — time taken so far: 1.21 seconds
#> ℹ 60% done — time taken so far: 1.31 seconds
#> ℹ 70% done — time taken so far: 1.87 seconds
#> ℹ 80% done — time taken so far: 1.97 seconds
#> ℹ 90% done — time taken so far: 2.22 seconds
#> ℹ 100% done — time taken so far: 2.26 seconds
#> ✔ Total time taken: 2.26 seconds
gr = TCRdist_to_igraph(result$edges_df, result$nodes_df)