## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("netZooR") ## ----message=FALSE,warning=FALSE---------------------------------------------- library(netZooR) ## ----message=FALSE,warning=FALSE---------------------------------------------- r = c(1,1,1,2,2,2,3,3,3,4,4); b = c(1,2,3,1,2,4,2,3,4,3,4); reds <- c("Alice","Sue","Janine","Mary") blues <- c("Bob","John","Ed","Hank") elist <- data.frame(red=reds[r], blue=blues[b]) ## ----message=FALSE,warning=FALSE---------------------------------------------- condor.object <- createCondorObject(elist) ## ----message=FALSE,warning=FALSE---------------------------------------------- names(condor.object) ## ----message=FALSE,warning=FALSE---------------------------------------------- condor.object <- condorCluster(condor.object) print(condor.object$red.memb) print(condor.object$blue.memb) ## ----message=FALSE,warning=FALSE---------------------------------------------- gtoy = graph.edgelist(as.matrix(elist),directed=FALSE) set.graph.attribute(gtoy, "layout", layout.kamada.kawai(gtoy)) V(gtoy)[c(reds,blues)]$color <- c(rep("red",4),rep("blue",4)) ## ----fig=TRUE,message=FALSE,warning=FALSE------------------------------------- plot(gtoy,vertex.label.dist=2) ## ----message=FALSE,warning=FALSE---------------------------------------------- condor.object <- condorQscore(condor.object) ## ----fig=TRUE,message=FALSE,warning=FALSE------------------------------------- q_women <- condor.object$qscores$red.qscore core_stats <- condorCoreEnrich(test_nodes=c("Alice","Mary"), q=q_women,perm=TRUE,plot.hist=TRUE) ## ----message=FALSE,warning=FALSE---------------------------------------------- data(small1976) condor.object <- createCondorObject(small1976) condor.object <- condorCluster(condor.object, project=FALSE) ## ----fig=TRUE,message=FALSE,warning=FALSE------------------------------------- condorPlotHeatmap(condor.object) ## ----------------------------------------------------------------------------- sessionInfo()