igraph

问题 I am trying to find an efficient (i.e. avoid using loops) way to apply a function that iteratively takes as arguments the current and previous (or next) elements of a list and returns a lists of the result (the length of which will necessarily be 1 element shorter). As a concrete example, I have a list of vertices defining a path in some graph vlist <- c(1,2,7,12,17) which come from a lattice graph constructed using the igraph function "lattice" G <- graph.lattice(c(5,7)) I want to apply the

问题 This question already has an answer here : Arrange base plots and grid.tables on the same page (1 answer) Closed 3 years ago . How can we plot Network plot ( igraph package plot ) and Venn diagram ( VennDiagram gList object ) side-by-side in one PDF page ? Tried to follow below solutions, didn't work: Plot gList side by side Plot 2 tmap objects side-by-side Side-by-side Venn diagram using Vennerable Here is an example, which plots them in two pages. I used grid.newpage() to make it plot in

问题 So I am using all_shortest_paths to get an output, which looks like this: PathsE $res[[1]] + 4/990 vertices, named: [1] Sortilin GGA1 Ubiquitin PIMT $res[[2]] + 4/990 vertices, named: [1] Sortilin TrkA PLK1 PIMT $res[[3]] + 4/990 vertices, named: [1] Sortilin APP JAB1 PIMT I would like to turn this into a dataframe so that I can manipulate it. For reference, I would like the dataframe to look like this: Prot1 Prot2 Prot3 Prot4 Pathway1 Sortilin GGA1 PLK1 PIMT Pathway2 Sortilin TrkA PLK1 PIMT

问题 I am interested in visualizing pathways patients have based on a pre-specified list of events (e.g. diagnosis, surgery, treatment1, treatment2, death). A test data set might look like this: df <- structure(list(ID = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L), .Label = c("a", "b", "c"), class = "factor"), Event = structure(c(2L, 3L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 5L, 1L), .Label = c("death", "diagnosis", "surgery", "treatment1", "treatment2"), class = "factor"), date =

问题 Building off this question here, is there a way to extend this subgraph to include vertices connected by two degrees to a subset of vertices? I'm thinking of a command similar to the functions in make_ego_graph() where order=2 and mode="in". I'm working with a directed graph object. Thus far, I've come up with the following, but it's not producing the graph I'm looking for. first_degree <- V(graph)$condition == "something" second_degree <- V(graph)[to(first_degree)] edges_subset <- E(graph)

问题 I have a data.frame with 93 millon elements and 3 numeric variables. The third variable, "component" groups some rows by an id. The data consists of an edge list of a huge graph, the component number indicates the rows that belong to the same connected component. There are about 83 million such components. I am now trying t split the data frame into a list 83 million of data.frames. I do this in order to apply some igraph functions to each component. This SO answer indicates that split() is

问题 I have a python application primarily dependent on matplotlib, tkinter, numpy and scipy I have been distributing for multiple operating systems. I build these on top of the python.org version of python 2.6. For mac, I have had good success in the past with py2app and pyinstaller to build standalone versions of my application. Recently, however, I have included functions that require patsy, pandas and igraph and have had to move to the mac distributed version of python 2.6 in order to get

问题 I would like to use igraph to find edge sequences corresponding to branches from a tree. Ideally, I would like to retain the branches in a data frame. Consider this example: library(igraph) g <-erdos.renyi.game(50, 3/50) mg <- minimum.spanning.tree(g) diam <- get.diameter(mg) E(mg)$color = "black" E(mg, path = diam)$color = "purple" E(mg, path = diam)$width = 6 plot(mg) Here the main path is diam , the purple line. Mr. Flick already kindly answered how to find the edges which are incident on

问题 enter image description here I have tried this code of tripartite graph. but i have to use .csv file library(igraph) data = "From, To Recipe:Chicken Marsala,flour Recipe:Chicken Marsala,sage Recipe:Chicken Marsala,chicken Recipe:Chicken Marsala,wine Recipe:Chicken Marsala,butter Recipe:Glazed Carrots,butter Recipe:Glazed Carrots,vinegar Recipe:Glazed Carrots,carrot Recipe:Glazed Carrots,chive flour,compound:X2 sage,compound:X3 chicken,compound:X6 chicken,compound:X7 wine,compound:X1 wine

问题 I am attempting to assign attributes to the vertices in my network. The code I am using is: g2 <- graph.data.frame(edgelist2014, vertices=nodelabels2014, directed=FALSE) where edgelist2014 is an edgelist with 514,000+ observations in this format: fromRespondent toRespondent weight 1 2 6 1 3 4 ... ... ... 1014 1015 7 and nodelabels2014 is a data frame where the first column is fromRespondent and lists 1 - 1015 followed by 14 columns of attribute data. I have also tried this with 1 - 1014. I