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 > >
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