## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## For links library("BiocStyle") ## Track time spent on making the vignette #startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], DT = citation("DT")[1], ggplot2 = citation("ggplot2")[1], golem = citation("golem")[1], knitr = citation("knitr")[3], plotly = citation("plotly")[1], RColorBrewer = citation("RColorBrewer")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], shiny = citation("shiny")[1], testthat = citation("testthat")[1], biocthis = citation("biocthis")[1], shinyjs = citation("shinyjs")[1], shinyFiles = citation("shinyFiles")[1], plyr = citation("plyr")[1], data.table = citation("data.table")[1], stringr = citation("stringr")[1], stringdist = citation("stringdist")[1], plot3D = citation("plot3D")[1], gridExtra = citation("gridExtra")[1], dplyr = citation("dplyr")[1], shinyBS = citation("shinyBS")[1], fs = citation("fs")[1] ) ## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) ## ----echo=FALSE, out.width='50%', fig.align='center'-------------------------- knitr::include_graphics(path = system.file("app", "www", "tripr.png", package="tripr", mustWork=TRUE)) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("tripr") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----setup-------------------------------------------------------------------- library(tripr) ## ----demostart, eval=FALSE---------------------------------------------------- # tripr::run_app() ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "upload_data.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Preselection.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Preselection_Clean_table.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Selection.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Selection_visual.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "pipeline_overview.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Clonotypes_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "clonotypes_tab.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "highly_similar_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "highly_sim_clono_tab.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "repertoires_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "repertoires_tab.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "mv_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "multiple_tab.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "insert_identity_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "Alignment_pipeline.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "alignment_tab.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "visual_clono.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "hist3d_visual.png", package="tripr", mustWork=TRUE)) ## ----echo=FALSE, out.width='100%', fig.align='center'------------------------- knitr::include_graphics(path = system.file("app", "www", "overview.png", package="tripr", mustWork=TRUE)) ## ----eval = FALSE------------------------------------------------------------- # ?tripr::run_TRIP ## ----eval=FALSE--------------------------------------------------------------- # fs::path_package("extdata", "dataset", package = "tripr") ## ----eval=FALSE--------------------------------------------------------------- # c("1_Summary.txt", "2_IMGT-gapped-nt-sequences.txt", # "4_IMGT-gapped-AA-sequences.txt", "6_Junction.txt") ## ----eval=FALSE--------------------------------------------------------------- # datapath <- fs::path_package("extdata", "dataset", package="tripr") # output_path <- tools::R_user_dir("tripr", which="cache") # cell <- "Bcell" # preselection <- "1,2,3,4C:W" # selection <- "5" # filelist <- c("1_Summary.txt", # "2_IMGT-gapped-nt-sequences.txt", # "4_IMGT-gapped-AA-sequences.txt", # "6_Junction.txt") # throughput <- "High Throughput" # preselection <- "1,2,3,4C:W" # selection <- "5" # identity_range <- "88:100" # pipeline <- "1" # select_clonotype <- "V Gene + CDR3 Amino Acids" # # run_TRIP( # datapath=datapath, # output_path=output_path, # filelist=filelist, # cell=cell, # throughput=throughput, # preselection=preselection, # selection=selection, # identity_range=identity_range, # pipeline=pipeline, # select_clonotype=select_clonotype) ## ----'citation'--------------------------------------------------------------- ## Citation info citation("tripr") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo() ## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE---- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))