We can't reproduce your code because we don't have your data. You also don't show any error messages you receive, or how the output/result is different than what you expect to see.
On Wed, Feb 4, 2015 at 5:30 PM, Benika H <[email protected]> wrote: > Hi Tamas, Could you help me with my question. > > I have an edgelist (1st file) which I created the graph object. I want to > use walktrap community detection on that network. After getting the > communities, I need to plot only the communities with at most 8 vertices > and at least 2 vertices (no isolates). Using those communities, I want to > join the edgelist from the 2nd file to the matching vertices in a column. > Here, I think I can use graph.union. However, I can't seem to get the > communities with a sizes 2-8.. > > > > My data are in files: > hgnc_mapped looks like > > ABCB7 MARS 0.054839 > ABCB7 MAX 0.0638109 > ABCB7 MRPS34 0.112394 > ABCB7 NDUFA8 0.123633 > ABCB7 NUP133 0.0810968 > > combined looks like > > hsa-mir-1180 MAPK7 > hsa-mir-1228 NACA > hsa-mir-1248 IRF9 > hsa-mir-1248 PSME2 > hsa-mir-1254 KIAA1279 > hsa-mir-125b-1PCDHGB3 > > My code so far is: > > edgeList <- read.table("hgnc_mapped.txt", header=TRUE, sep="\t") > eQTLList <- read.table("combined.txt", header=TRUE, sep="\t") > t <- as.data.frame(edgeList) > u <- as.data.frame(eQTLList) > > y <- graph.data.frame(t, directed=FALSE, vertices=NULL) > V(y) > z <- graph.data.frame(u, directed=TRUE) > # new_g <- delete.vertices(y,which(degree(y) < 1) - 1) > # V(new_g) > ``` > > ```{r cache=TRUE, dependson='network-data'} > #Run the community detection algorithm > wc <- walktrap.community(y, weights = edgeList$Weight, steps=6, merges > =TRUE, modularity = TRUE, membership = TRUE) > ``` > > c1 <- clusters(y) > c1$membership > # small.clusters <- which(c1$size > 7) > # vertices.to.delete <- which((c1$membership)==small.clusters)-1 > # g <- delete.vertices(y, vertices.to.delete) > layout <- layout.fruchterman.reingold(y) > x <- (which(c1$csize) < 8 & (c1$csize) > 1) > vertices <- which(c1$membership==x) > g1 <- induced.subgraph(y, vertices) > plot(g1,layout=layout[vertices,]) > > Thanks in advance..... > > >> > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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