## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library('knitcitations') ## Load knitcitations with a clean bibliography cleanbib() cite_options(hyperlink = 'to.doc', citation_format = 'text', style = 'html') # Note links won't show for now due to the following issue # https://github.com/cboettig/knitcitations/issues/63 ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation('BiocStyle'), derfinder = citation('derfinder')[1], derfinderPlot = citation('derfinderPlot')[1], sessioninfo = citation('sessioninfo'), GenomicRanges = citation('GenomicRanges'), knitcitations = citation('knitcitations'), knitr = citation('knitr')[3], rmarkdown = citation('rmarkdown'), rtracklayer = citation('rtracklayer'), testthat = citation('testthat'), ggplot2 = citation('ggplot2'), cowplot = citation('cowplot'), BSgenome.Hsapiens.UCSC.hg19 = citation('BSgenome.Hsapiens.UCSC.hg19'), Biostrings = citation('Biostrings'), RColorBrewer = citation('RColorBrewer'), bumphunter = citation('bumphunter')[1], GenomicState = citation('GenomicState') ) write.bibtex(bib, file = 'brainflowprobes_ref.bib') ## ----'install', eval = FALSE----------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("brainflowprobes") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() # # ## If you want to force the installation of the development version, you can # ## do so by running. However, we suggest that you wait for Bioconductor to # ## run checks and build the latest release. # BiocManager::install("LieberInstitute/brainflowprobes") ## ----'citation'------------------------------------------------------------ ## Citation info citation('brainflowprobes') ## ----'start', message=FALSE------------------------------------------------ ## Load brainflowprobes R package library('brainflowprobes') ## ----'annotate'------------------------------------------------------------ region_info("chr2:162279880-162282378:+", CSV = FALSE, SEQ = TRUE, OUTDIR = ".") ## ----'visualize coverage', eval = FALSE------------------------------------ # plot_coverage("chr2:162279880-162282378:+", # PDF = "regionCoverage_fractionedData.pdf", # OUTDIR = '.', # COVERAGE = NULL, VERBOSE = FALSE) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 850------- knitr::include_graphics('regionCoverage_fractionedData.pdf') ## ----'visualize shorter region coverage', eval = FALSE--------------------- # plot_coverage("chr2:162280900-162282378:+", # PDF = "regionCoverage_fractionedData_shorter.pdf", # OUTDIR = '.', # COVERAGE = NULL, VERBOSE = FALSE) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 850------- knitr::include_graphics('regionCoverage_fractionedData_shorter.pdf') ## ----'precalculate coverage', eval = FALSE--------------------------------- # tbr1.cov <- brainflowprobes_cov("chr2:162280900-162282378:+", VERBOSE = FALSE) ## ----'plot four panels', eval = FALSE-------------------------------------- # four_panels("chr2:162280900-162282378:+", # PDF = "four_panels.pdf", # OUTDIR = '.', # JUNCTIONS = FALSE, # COVERAGE = tbr1.cov, VERBOSE = FALSE) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 1000------ knitr::include_graphics('four_panels.pdf') ## ----'annotate multiple'--------------------------------------------------- candidates <- c( "chr2:162279880-162282378:+", "chr11:31806351-31811553", "chr7:103112236-103113354" ) region_info(candidates, CSV = FALSE, SEQ = FALSE) ## ----'plot multiple', eval=FALSE------------------------------------------- # plot_coverage(candidates, # PDF = "regionCoverage_fractionedData_multiple.pdf", OUTDIR = '.') # # four_panels(candidates, PDF = "four_panels_multiple.pdf", OUTDIR = '.') ## ----'PENK', eval=FALSE---------------------------------------------------- # PENK_exons <- c( # 'chr8:57353587-57354496:-', # 'chr8:57358375-57358515:-', # 'chr8:57358985-57359040:-', # 'chr8:57359128-57359292:-' # ) # # four_panels(PENK_exons, JUNCTIONS = TRUE, PDF = 'PENK_panels.pdf') ## ----createVignette, eval=FALSE-------------------------------------------- # ## Create the vignette # library('rmarkdown') # system.time(render('brainflowprobes-vignette.Rmd', 'BiocStyle::html_document')) # # ## Extract the R code # library('knitr') # knit('brainflowprobes-vignette.Rmd', tangle = TRUE) ## ----createVignette2------------------------------------------------------- ## Clean up file.remove('brainflowprobes_ref.bib') ## ----reproduce1, echo=FALSE------------------------------------------------ ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE------------------------------------------------ ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits=3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library('sessioninfo') options(width = 120) session_info() ## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography bibliography()