Hi Chris, It said my email was too large.
Here is a snippet. 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 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,]) I've tried it with an extra set. I will try it again. Thanks Chris, On Wed, Feb 4, 2015 at 6:01 PM, Chris Watson <[email protected]> wrote: > You need to adjust the placement of your parentheses so they include the > full logical expression. > > On Wed, Feb 4, 2015 at 5:48 PM, Benika H <[email protected]> wrote: > >> Also, just got an error >> >> Error in which(c1$csize) : argument to 'which' is not logical >> Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval >> -> which >> Execution halted >> >> >> >> >> >> On Wed, Feb 4, 2015 at 5:45 PM, Benika H <[email protected]> >> wrote: >> >>> Oh ok. I'm new to this. I will send data. >>> >>> hgnc_mapped2.txt is the 1st edgelist (y in my code) >>> newdata.txt is the 2nd edgelist (z in my code) >>> >>> I got an error saying *Warning in layout[, 1] + label.dist * >>> cos(-label.degree) * (vertex.size +## : longer object length is not a >>> multiple of shorter object length* >>> I'm not getting any errors now, but I'm still getting all communities >>> except thrones I requested. >>> >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Feb 4, 2015 at 5:33 PM, Chris Watson <[email protected]> >>> wrote: >>> >>>> 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 >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> igraph-help mailing list >>>> [email protected] >>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>> >>>> >>> >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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