# #——回声= FALSE ------------------------------------------------------------ knitr: opts_chunk设置(eval =假美元 ) ## ---- 设置 -------------------------------------------------------------------- # # suppressPackageStartupMessages(库(dplyr)) # # suppressPackageStartupMessages(库(RCy3)) # # suppressPackageStartupMessages(库(KEGGREST)) # # Sys.setenv(语言=“en_US.UTF-8”)#库(transomics2cytoscape) # networkDataDir <——tempfile ();dir.create(networkDataDir) # # networkLayers <- system. xml文件(“extdata / usecase1”、“yugi2014。Tsv "， # package = "transomics2cytoscape") # stylexml <- system。文件(“extdata / usecase1”、“yugi2014。xml", # package = "transomics2cytoscape") # suid <- create3Dnetwork(networkDataDir, networkLayers, stylexml) # # layer1to2 <- system.file("extdata/usecase1", "k2e.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer1to2) # # layer3to2 <- system.file("extdata/usecase1", "allosteric_ecnumber.tsv", # package = "transomics2cytoscape") # ec2reaction(layer3to2, 6, "allosteric_ec2rea.tsv") # suid <- createTransomicEdges(suid, "allosteric_ec2rea.tsv") ## ----------------------------------------------------------------------------- # ecnum <- system.file("extdata", "allosteric_ecnumber.tsv", # package = "transomics2cytoscape") # ec2reaction(ecnum, 6, "allosteric_ec2rea.tsv") ## ----------------------------------------------------------------------------- # networkDataDir <- tempfile(); dir.create(networkDataDir) # tfs <- system.file("extdata/usecase2", "TFs.sif", # package = "transomics2cytoscape") # file.copy(tfs, networkDataDir) # networkLayers <- system.file("extdata/usecase2", "kokaji2020.tsv", # package = "transomics2cytoscape") # stylexml <- system.file("extdata/usecase2", "Kokaji2020styles.xml", # package = "transomics2cytoscape") # suid <- create3Dnetwork(networkDataDir, networkLayers, stylexml) # # layer1to2 <- system.file("extdata/usecase2", "s2t_name_updated.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer1to2) # # layer2to3 <- system.file("extdata/usecase2", "t2e_name_updated.tsv", # package = "transomics2cytoscape") # suid <- createTransomicEdges(suid, layer2to3) # # layer3to4 <- system.file("extdata/usecase2", "e2r_updated.tsv", # package = "transomics2cytoscape") # ec2reaction(layer3to4, 6, "e2r_updated_ec2rea.tsv") # suid <- createTransomicEdges(suid, "e2r_updated_ec2rea.tsv") # # layer5to4 <- system.file("extdata/usecase2", "m2r_updated.tsv", # package = "transomics2cytoscape") # ec2reaction(layer5to4, 6, "m2r_updated_ec2rea.tsv") # suid <- createTransomicEdges(suid, "m2r_updated_ec2rea.tsv") ## ----------------------------------------------------------------------------- # sessionInfo()