## ---- echo = TRUE, results = 'hide'， message = FALSE, warning = FALSE--------- library(SBGNview) library(summarizeexperiment) data("IFNg"， " paths .info")计数。data <- assays(IFNg)$counts head(count.data) wt.cols <- which(IFNg$group == "wt") ko。cols <- which(IFNg$group == "ko") ## ---- echo = TRUE, results = 'hide'， message = FALSE, warning = FALSE------ ensembl。路径<- sbgn.gsets(id. gsets)type = "ENSEMBL"， species = "mmu"， mol.type = "gene"， output.path .name = TRUE) head(ENSEMBL .pathway[[2]]) ## ---- echo = TRUE, results = 'hide'， message = FALSE, warning = FALSE--------- if(!requireNamespace("gage"， quiet = TRUE)) {BiocManager::install("gage"， update = FALSE)} library(gage) degs <- gage(exprs = count. count);数据，gsets =集合。路径，ref = wt.cols, samp = ko。Cols, compare = "paired" #"as。Group ") head(degs$greater)[，3:5] head(degs$less)[，3:5] down。pathways <- row.names(degs$less)[1:10] head(down. paths) ## ---- echo = TRUE, results = 'hide'， message = FALSE, warning = FALSE--------- ensembl. pathskoVsWt <- count.data[，ko.cols]-count.data[，wt. cols]或者，我们也可以计算每个基因的平均折叠变化，这与上面的测量分析相对应，使用compare="as。集团”的意思。Wt <- apply(count.data[， Wt .data])Cols]，1，"mean")头(mean.wt)ko <- apply(count.data[，ko.cols]，1，"mean") head(mean.ko) #丰度值为对数刻度。 Hence fold change is their difference. ensembl.koVsWt.m <- mean.ko - mean.wt ## ---- echo = TRUE, results = 'hide', message = FALSE, warning = FALSE--------- #load the SBGNview pathway collection, which may takes a few seconds. data(sbgn.xmls) down.pathways <- sapply(strsplit(down.pathways,"::"), "[", 1) head(down.pathways) sbgnview.obj <- SBGNview( gene.data = ensembl.koVsWt, gene.id.type = "ENSEMBL", input.sbgn = down.pathways[1:2],#can be more than 2 pathways output.file = "ifn.sbgnview.less", show.pathway.name = TRUE, max.gene.value = 2, min.gene.value = -2, mid.gene.value = 0, node.sum = "mean", output.format = c("png"), font.size = 2.3, org = "mmu", text.length.factor.complex = 3, if.scale.compartment.font.size = TRUE, node.width.adjust.factor.compartment = 0.04 ) sbgnview.obj ## ----ifng, echo = FALSE,fig.cap="\\label{fig:ifng}SBGNview graph of the most down-regulated pathways in IFNg KO experiment"---- library(knitr) include_graphics("ifn.sbgnview.less_R-HSA-877300_Interferon gamma signaling.svg") ## ----ifna, echo = FALSE,fig.cap="\\label{fig:ifna}SBGNview graph of the second most down-regulated pathways in IFNg KO experiment"---- library(knitr) include_graphics("ifn.sbgnview.less_R-HSA-909733_Interferon alpha_beta signaling.svg") ## ---- 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", output.format = c("png"), font.size = 2.3, org = "hsa", text.length.factor.complex = 3, if.scale.compartment.font.size = TRUE, node.width.adjust.factor.compartment = 0.04 ) sbgnview.obj ## ----cancerds, 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()