## ---- eval=TRUE, echo=TRUE, results='hide', message=FALSE--------------------- library(PanVizGenerator) getGO() ## ---- eval=FALSE-------------------------------------------------------------- # PanVizGenerator() ## ---- echo=TRUE, eval=TRUE, warning=FALSE------------------------------------- csvFile <- system.file('extdata', 'exampleData.csv', package = 'PanVizGenerator') outputDir <- tempdir() # Generate the visualization panviz(csvFile, location = outputDir) ## ---- echo=TRUE, eval=TRUE, warning=FALSE------------------------------------- # Get data from csv pangenome <- read.csv(csvFile, quote='', stringsAsFactors = FALSE) name <- pangenome$name go <- pangenome$go ec <- pangenome$ec pangenome <- pangenome[, !names(pangenome) %in% c('name', 'go', 'ec')] # Annotation can come in many ways # This is valid head(go) # And this is valid too head(strsplit(go, '; ')) # Or another delimiter head(gsub('; ', 'delimiter', go)) # Generate the visualization panviz(pangenome, name=name, go=go, ec=ec, location=outputDir) ## ---- echo=TRUE, eval=TRUE, warning=FALSE, message=FALSE---------------------- # Get an example pangenome with annotation library(FindMyFriends) pangenome <- .loadPgExample(withNeighborhoodSplit = TRUE) annotation <- readAnnot(system.file('extdata', 'examplePG', 'example.annot', package = 'FindMyFriends')) head(annotation) pangenome <- addGroupInfo(pangenome, annotation, key = 'name') pangenome # Generate the visualization panviz(pangenome, location = outputDir) ## ---- echo=TRUE, eval=TRUE, warning=FALSE------------------------------------- panviz(pangenome, location = outputDir, consolidate = FALSE) ## ---- echo=TRUE, eval=FALSE, warning=FALSE------------------------------------ # panviz(pangenome, location = outputDir, showcase = TRUE) ## ---- echo=TRUE, eval=TRUE, warning=FALSE------------------------------------- panviz(pangenome, location = outputDir, dist = 'binary', clust = 'complete', center = FALSE, scale = FALSE) ## ---- echo=FALSE, eval=TRUE--------------------------------------------------- sessionInfo()