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Moving around a tree
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| library(tidyverse) | |
| library(igraph) | |
| ###Fake Taxonomy | |
| g <- make_tree(20, 2) %>% | |
| set_edge_attr('arrow.size', value = .5) %>% | |
| set_vertex_attr('name', value = 1:vcount(.)) %>% | |
| set_vertex_attr('label.cex', value = .7) %>% | |
| set_graph_attr('layout', layout_as_tree(.)) | |
| plot(g) | |
| ####Choose something | |
| n4 <- V(g)[name == '4'] | |
| g %>% | |
| plot( | |
| vertex.color = ifelse(V(.) %in% n4, 'gold', 'white'), | |
| main = "Node 4 is our node of interest." | |
| ) | |
| ######Prune tree | |
| n4Children <- dfs(g, n4, neimode = 'out', unreachable = F) %>% | |
| .$order %>% | |
| .[!is.na(.)] | |
| g %>% | |
| plot( | |
| vertex.color = ifelse(V(.) %in% n4Children, 'gold', 'white'), | |
| edge.color = ifelse(E(.) %in% E(.)[from(n4Children)], 'black', 'lightgrey'), | |
| main = "What are node 4's children?" | |
| ) | |
| ######Roots | |
| n4Ancestors <- dfs(g, n4, neimode = 'in', unreachable = F) %>% | |
| .$order %>% | |
| .[!is.na(.)] | |
| g %>% | |
| plot( | |
| vertex.color = ifelse(V(.) %in% n4Ancestors, 'gold', 'white'), | |
| edge.color = ifelse(E(.) %in% E(.)[to(n4Ancestors)], 'black', 'lightgrey'), | |
| main = "What are node 4's ancestors?" | |
| ) | |
| ######Find Connections | |
| n4_n13 <- shortest_paths(g, '4', '13', mode = 'all', output = 'both') | |
| g %>% | |
| plot( | |
| vertex.color = ifelse(V(.) %in% n4_n13$vpath[[1]], 'gold', 'white'), | |
| edge.color = ifelse(E(.) %in% n4_n13$epath[[1]], 'black', 'lightgrey'), | |
| main = 'How are nodes 4 and 13 related?' | |
| ) | |
| ###### Let's add an ancestor | |
| g_0 <- g %>% | |
| {. + vertices("0") + edges('0', '1')} %>% | |
| set_graph_attr('layout', layout_as_tree(.)) | |
| plot(g_0) | |
| ####Let's have two trees....probably best to keep them as separate graphs though... | |
| g2 <- make_tree(20, 2) | |
| V(g)$alpha <- letters[seq(vcount(g))] | |
| V(g2)$alpha <- map_chr(seq(vcount(g)), function(i) ifelse(i < 16, letters[i], letters[36-i])) | |
| V(g)$tree = 1 | |
| V(g2)$tree = 2 | |
| V(g2)$name <- 1:vcount(g2) + 20 | |
| g3 <- graph_from_data_frame( | |
| rbind(as_data_frame(g) %>% select(from, to),as_data_frame(g2)), | |
| T, | |
| rbind(as_data_frame(g, 'vertices') %>% select(-label.cex), as_data_frame(g2, 'vertices') ) | |
| ) %>% | |
| set_edge_attr('arrow.size', value = .5) %>% | |
| set_vertex_attr('name', value = paste0('.',1:vcount(.))) %>% | |
| set_vertex_attr('label', value = V(.)$alpha) %>% | |
| set_graph_attr('layout', layout_as_tree(.)) | |
| ##### Find similar nodes from both trees | |
| plot(g3, | |
| vertex.color = ifelse(V(g3)$alpha == 'e', 'gold', 'white'), | |
| main = "How are the e nodes for each tree different?", | |
| asp = 0) | |
| eSubTree <- V(g3)[alpha == 'e'] %>% | |
| map(function(x){ | |
| dfs(g3, x, 'out', F) %>% | |
| .$order %>% | |
| .[!is.na(.)] %>% | |
| .$name | |
| }) %>% | |
| unlist %>% | |
| {V(g3)[.]} | |
| ##### find all their descendents for comparison | |
| g3 %>% | |
| plot( | |
| vertex.color = ifelse(V(.) %in% eSubTree, 'gold', 'white'), | |
| edge.color = ifelse(E(.) %in% E(.)[from(eSubTree)], 'black', 'lightgrey'), | |
| main = 'What are the descendent subgraphs of the e nodes?', | |
| asp = 0 | |
| ) | |
| #####Let's identify the differences | |
| g3 %>% | |
| {. - V(.)[!name %in% eSubTree$name]} %>% | |
| (function(x){ | |
| #components are basically two unattached subgraphs | |
| tempGroups <- x %>% | |
| components %>% | |
| groups() | |
| #if nodes are in all subgraphs/components/trees, then the number of nodes should match the number of trees | |
| tempDiff <- map(tempGroups, function(y){ | |
| V(x)[name %in% y]$alpha | |
| }) %>% | |
| unlist() %>% | |
| table() | |
| #If a nodes is not in all trees, then let's point focus on them | |
| diffNodes <- tempDiff %>% | |
| .[. != length(tempGroups)] %>% | |
| names %>% | |
| {V(x)[alpha %in% .]} | |
| plot( | |
| x, | |
| layout = layout_as_tree(x), | |
| vertex.color = ifelse(V(x) %in% diffNodes, 'gold', 'white'), | |
| vertex.frame.color = ifelse(V(x) %in% unlist(ego(x, 1, diffNodes)), 'red', 'black'), | |
| edge.color = ifelse(E(x) %in% E(x)[diffNodes %--% V(x)], 'red', 'lightgrey'), | |
| main = "What's the different between the two e subgraphs?", | |
| asp= 0 | |
| ) | |
| }) |
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