## ----install, eval = FALSE---------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("MagellanNTK") ## ----setup, message = FALSE--------------------------------------------------- library(MagellanNTK) ## ----keytermsOrganisation, results='markup', fig.cap="Visual representation of key terms", echo=FALSE, fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/keytermsOrganisation.png", error = FALSE) ## ----pipelinedemoOrganisation, results='markup', fig.cap="PipelineDemo's organisation", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/pipelinedemoOrganisation.png", error = FALSE) ## ----timelinelayout, results='markup', fig.cap="(a) Horizontal workflow timeline, (b) Vertical step timeline", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/timelinelayout.png", error = FALSE) ## ----history, results='markup', fig.cap="History table", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/history.png", error = FALSE) ## ----mainInterface, results='markup', fig.cap="General user interface: (a) Main sidebar, (b) Main interface", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterface.png", error = FALSE) ## ----menuSidebar, results='markup', fig.cap="The general menus of the main sidebar", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/menuSidebar.png", error = FALSE) ## ----mainInterfaceGeneral, results='markup', fig.cap="Main interface during a workflow: (a) Process sidebar, (b) Workflow header, (c) Content area", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterfaceGeneral.png", error = FALSE) ## ----mainInterfaceSidebar, results='markup', fig.cap="Composition of the process sidebar: (a) Pipeline name, (b) Process timeline, (c) Parameters", echo=FALSE, out.width='40%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterfaceSidebar.png", error = FALSE) ## ----mainInterfaceSidebarButtons, results='markup', fig.cap="The process sidebar's buttons: (a) 'Previous' button, (b) 'Reset' button, (c) 'Run' button, (d) 'Run ->' button, (e) 'Next' button", echo=FALSE, out.width='50%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterfaceSidebarButtons.png", error = FALSE) ## ----mainInterfaceHeader, results='markup', fig.cap="Composition of the workflow header: (a) Workflow timeline, (b) EDA button", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterfaceHeader.png", error = FALSE) ## ----mainInterfaceHeaderButtons, results='markup', fig.cap="The workflow header's buttons: (a) 'Go back to start' button, (b) 'Previous' and 'Next' buttons", echo=FALSE, out.width='40%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/mainInterfaceHeaderButtons.png", error = FALSE) ## ----lanchpipelinedemo, eval = FALSE------------------------------------------ # library(MagellanNTK) # wf.path <- system.file('workflow/PipelineDemo', package = 'MagellanNTK') # MagellanNTK(wf.path, 'PipelineDemo') ## ----homePage, results='markup', fig.cap="Home page", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/homePage.png", error = FALSE) ## ----opendataset, results='markup', fig.cap="Open a dataset", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_mod_open_dataset.png", error = FALSE) ## ----EDA1, results='markup', fig.cap="EDA 'Infos' tab", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_EDA1.png", error = FALSE) ## ----EDA2, results='markup', fig.cap="EDA 'History' tab", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_EDA2.png", error = FALSE) ## ----EDA3, results='markup', fig.cap="EDA 'EDA' tab", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_EDA3.png", error = FALSE) ## ----pipelinedescription, results='markup', fig.cap="Description step", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_PipelineDemo_Description.png", error = FALSE) ## ----datageneration3, results='markup', fig.cap="'Data generation' sub-step", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_PipelineDemo_DataGeneration3.png", error = FALSE) ## ----UIPipelineDemoPreprocessing2, results='markup', fig.cap="'Filtering' sub-step", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_PipelineDemo_Preprocessing2.png", error = FALSE) ## ----UIPipelineDemoPreprocessing3, results='markup', fig.cap="'Normalization' sub-step", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_PipelineDemo_Preprocessing3.png", error = FALSE) ## ----UIPipelineDemoClustering2, results='markup', fig.cap="'Clustering' sub-step", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/UI_PipelineDemo_Clustering2.png", error = FALSE) ## ----convertProcess, results='markup', fig.cap="Convert process", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/convertProcess.png", error = FALSE) ## ----saveProcess, results='markup', fig.cap="'Save as' tab", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/saveProcess.png", error = FALSE) ## ----resetastepbef, results='markup', fig.cap="Before resetting the 'Preprocessing' process", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/beforeResetingProcess.png", error = FALSE) ## ----resetastepaft, results='markup', fig.cap="After resetting the 'Preprocessing' process", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/afterresetPreprocessing.png", error = FALSE) ## ----launch, eval = FALSE----------------------------------------------------- # library(MagellanNTK) # wf.path <- system.file('workflow/PipelineDemo', package = 'MagellanNTK') # MagellanNTK(wf.path, 'PipelineDemo_Preprocessing') ## ----singleprocess, results='markup', fig.cap="'Preprocessing' process when launched as a single process", echo=FALSE, out.width='100%', fig.align='center', fig.wide = TRUE---- knitr::include_graphics("./figs/singleprocess.png", error = FALSE) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()