## ----echo = FALSE, eval = TRUE, results = 'hide', message = FALSE, warning = FALSE---- library(knitr) ## ----setup, eval = FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)){ # install.packages("BiocManager") # } # BiocManager::install(c("xml2", "rsvg", "igraph", "httr", "KEGGREST", "pathview", "gage", "SBGNview.data", "SummarizedExperiment", "AnnotationDbi")) ## ----depend, eval = FALSE----------------------------------------------------- # sudo apt install libxml2-dev libssl-dev libcurl4-openssl-dev librsvg2-dev ## ----install, eval = FALSE---------------------------------------------------- # BiocManager::install(c("SBGNview")) ## ----install.1, eval = FALSE-------------------------------------------------- # install.packages("devtools") # devtools::install_github("datapplab/SBGNview") ## ----clone.git, eval = FALSE-------------------------------------------------- # git clone https://github.com/datapplab/SBGNview.git ## ----echo = TRUE, eval = TRUE, results = 'hide', message = FALSE, warning = FALSE---- library(SBGNview) # load demo dataset, SBGN pathway data collection and info, which may take a few seconds data("gse16873.d","pathways.info", "sbgn.xmls") input.pathways <- findPathways("Adrenaline and noradrenaline biosynthesis") SBGNview.obj <- SBGNview( gene.data = gse16873.d[,1:3], gene.id.type = "entrez", input.sbgn = input.pathways$pathway.id, output.file = "quick.start", output.formats = c("png") ) print(SBGNview.obj) ## ----quickStartFig, echo = FALSE,fig.cap="\\label{fig:quickStartFig}Quick start example: Adrenaline and noradrenaline biosynthesis pathway. "---- include_graphics("quick.start_P00001.svg") ## ----echo = TRUE, eval = TRUE, results = 'hide', message = FALSE, warning = FALSE---- outputFile(SBGNview.obj) <- "quick.start.highlights" SBGNview.obj + highlightArcs(class = "production",color = "red") + highlightArcs(class = "consumption",color = "blue") + highlightNodes(node.set = c("tyrosine", "(+-)-epinephrine"), stroke.width = 4, stroke.color = "green") + highlightPath(from.node = "tyrosine", to.node = "dopamine", from.node.color = "green", to.node.color = "blue", shortest.paths.cols = "purple", input.node.stroke.width = 6, path.node.stroke.width = 5, path.node.color = "purple", path.stroke.width = 5, tip.size = 10 ) ## ----quickStartFigHighlight, echo = FALSE,fig.cap="\\label{fig:quickStartFigHighlight}Quick start example: Highlight arcs, nodes, and path."---- include_graphics("quick.start.highlights_P00001.svg") ## ----------------------------------------------------------------------------- sessionInfo()