## ----install, eval = FALSE---------------------------------------------------- # BiocManager::install(c("SBGNview")) ## ----installGage, eval = FALSE------------------------------------------------ # BiocManager::install(c("gage")) ## ---- echo = TRUE, results = 'hide', message = FALSE, warning = FALSE--------- library(SBGNview) library(SummarizedExperiment) library(SBGNview.data) data("IFNg") count.data <- assays(IFNg)$counts wt <- colnames(IFNg)[IFNg$group == "wt"] ko <- colnames(IFNg)[IFNg$group == "ko"] head(count.data) ## ---- echo = TRUE , results = 'hide', message = FALSE, warning = FALSE------ ensemble.to.pathway <- getMolList( database = "pathwayCommons" ,mol.list.ID.type = "ENSEMBL" ,org = "mmu" ,cpd.or.gene = "gene" ,output.pathway.name = TRUE ) head(ensemble.to.pathway[[2]]) ## ---- echo = TRUE, results = 'hide', message = FALSE, warning = FALSE--------- library(gage) degs <- gage(exprs = count.data ,gsets = ensemble.to.pathway ,ref = which(colnames(count.data) %in% wt) ,samp = which(colnames(count.data) %in% ko) ,compare = "as.group" ) head(degs$greater)[,c(1,4:5)] head(degs$less) down.pathways <- degs$less head(down.pathways) ## ---- echo = TRUE, results = 'hide', message = FALSE, warning = FALSE--------- mean.wt <- apply(count.data[,wt] ,1 ,"mean") head(mean.wt) mean.ko <- apply(count.data[,ko],1,"mean") head(mean.ko) ensemble.to.koVsWt <- mean.ko - mean.wt head(ensemble.to.koVsWt) ## ---- echo = TRUE, results = 'hide', message = FALSE, warning = FALSE--------- down.pathways <- do.call(rbind,strsplit(row.names(down.pathways),"::"))[,1] head(down.pathways) sbgnview.obj <- SBGNview( gene.data = ensemble.to.koVsWt, gene.id.type = "ENSEMBL", input.sbgn = down.pathways[1], output.file = "ifn.sbgnview.less", show.pathway.name = TRUE, max.gene.value = 2, min.gene.value = -2, mid.gene.value = 0, node.sum = "mean", label.spliting.string = c("-","_"," "), output.format = c("png"), inhibition.edge.end.shift = 1, font.size = 2, logic.node.font.scale = 6, font.size.scale.compartment = 1.5, org = "mmu", text.length.factor.macromolecule = 0.8, text.length.factor.compartment = 2, text.length.factor.complex = 3, if.scale.compartment.font.size = TRUE, node.width.adjust.factor.compartment = 0.058 ) sbgnview.obj ## ----ifnSBGNview, echo = FALSE,fig.cap="\\label{fig:SBGNview map from sbgnview}SBGNview"---- library(knitr) include_graphics("ifn.sbgnview.less_R-HSA-877300_Interferon gamma signaling.svg") ## ---- eval=FALSE, echo = TRUE, results = 'hide', message = FALSE, warning = FALSE---- # data("cancer.ds") # sbgnview.obj <- SBGNview( # gene.data = cancer.ds, # gene.id.type = "ENTREZID", # input.sbgn = "R-HSA-877300", # output.file = "demo.SummarizedExperiment", # show.pathway.name = TRUE, # max.gene.value = 1, # min.gene.value = -1, # mid.gene.value = 0, # node.sum = "mean", # label.spliting.string = c("-","_"," "), # output.format = c("png"), # # inhibition.edge.end.shift = 1, # font.size = 2, # logic.node.font.scale = 6, # font.size.scale.compartment = 1.5, # org = "hsa", # # text.length.factor.macromolecule = 0.8, # text.length.factor.compartment = 2, # text.length.factor.complex = 3, # if.scale.compartment.font.size = TRUE, # node.width.adjust.factor.compartment = 0.058 # ) # sbgnview.obj # ## ----cancerds,eval=FALSE, echo = FALSE,fig.cap="\\label{fig:cancerds}SBGNview of a cancer dataset gse16873"---- # include_graphics("demo.SummarizedExperiment_R-HSA-877300_Interferon gamma signaling.svg") ## ----------------------------------------------------------------------------- sessionInfo()