## ----pre, echo=FALSE, results='hide'------------------------------------------ library(knitr) opts_chunk$set(warning=FALSE, message=FALSE, cache=TRUE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----------------------------------------------------------------------------- library(rrvgo) go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo")) simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel") ## ----------------------------------------------------------------------------- scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID) reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db") ## ----------------------------------------------------------------------------- heatmapPlot(simMatrix, reducedTerms, annotateParent=TRUE, annotationLabel="parentTerm", fontsize=6) ## ----------------------------------------------------------------------------- scatterPlot(simMatrix, reducedTerms) ## ----eval=FALSE--------------------------------------------------------------- # treemapPlot(reducedTerms) ## ----------------------------------------------------------------------------- wordcloudPlot(reducedTerms, min.freq=1, colors="black") ## ----eval=FALSE--------------------------------------------------------------- # rrvgo::shiny_rrvgo() ## ----eval=FALSE--------------------------------------------------------------- # my_new_fancy_orgdb_object <- 'org.Zz.eg.db' # hsGO <- GOSemSim::godata(my_new_fancy_orgdb_object, ont="MF") ## ----citation----------------------------------------------------------------- citation("rrvgo") ## ----echo=FALSE--------------------------------------------------------------- sessionInfo()