## ----eval=FALSE, fig.height=6, fig.width=6------------------------------------ # library(levi) # LEVIui(browser=TRUE) #Launch Levi to Browser. # LEVIui(browser=FALSE) #Launch Levi to R environment. # ## ----eval=TRUE, fig.height=6, fig.width=6------------------------------------- library(levi) template_network <- file.path(system.file(package="levi"),"extdata", "medusa.dat", fsep = .Platform$file.sep) template_expression <- file.path(system.file(package="levi"), "extdata","expression.dat", fsep = .Platform$file.sep) multicolor <- levi(networkCoordinatesInput = template_network, expressionInput = template_expression, fileTypeInput = "dat", geneSymbolnput = "ID", readExpColumn= readExpColumn("TumorCurrentSmoker-NormalNeverSmoker"), contrastValueInput = 50, resolutionValueInput = 50, zoomValueInput = 50, smoothValueInput = 50, contourLevi = TRUE) twocolors <- levi(networkCoordinatesInput = template_network, expressionInput = template_expression, fileTypeInput = "dat", geneSymbolnput = "ID", readExpColumn= readExpColumn("TumorCurrentSmoker-NormalNeverSmoker"), setcolor = "pink_green", contourLevi = FALSE) ## ----eval=TRUE,fig.height=6, fig.width=6-------------------------------------- library(levi) base <- readExpColumn("TumorFormerSmoker-NormalFormerSmoker", "TumorNeverSmoker-TumorNeverSmoker") template_network <- file.path(system.file(package="levi"),"extdata", "medusa.dat", fsep = .Platform$file.sep) template_expression <- file.path(system.file(package="levi"), "extdata","expression.dat", fsep = .Platform$file.sep) multicolor <- levi(networkCoordinatesInput = template_network, expressionInput = template_expression, fileTypeInput = "dat", geneSymbolnput = "ID", readExpColumn= base, contrastValueInput = 50, resolutionValueInput = 50, zoomValueInput = 50, smoothValueInput = 50, contourLevi = FALSE) twocolors <- levi(networkCoordinatesInput = template_network, expressionInput = template_expression, fileTypeInput = "dat", geneSymbolnput = "ID", readExpColumn= base, setcolor = "pink_green", contourLevi = FALSE) ## ----eval=TRUE, label='Session information', , echo=FALSE--------------------- sessionInfo()