## ----init, echo=FALSE, results='hide'----------------------------------------- ## crop=NULL or FALSE => fix vignette rendering based on yihui/knitr#1796 ## added also error=FALSE to include_graphics knitr::opts_chunk$set( collapse = TRUE, tidy = FALSE, ## comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) ## check the output type out_type <- knitr::opts_knit$get("rmarkdown.pandoc.to") if (is.null(out_type)) out_type <- "html" ## add styling if (out_type == "html") { BiocStyle::markdown() ## BiocStyle::markdown(css.files = c('custom.css')) } else if (out_type == "latex") { BiocStyle::latex() } ## ----library------------------------------------------------------------------ library(seqLogo) ## ----makePWM------------------------------------------------------------------ mFile <- system.file("extdata/pwm1", package="seqLogo") m <- read.table(mFile) m p <- makePWM(m) ## ----slots-------------------------------------------------------------------- slotNames(p) pwm(p) ic(p) consensus(p) ## ----seqLogo1, fig.height=4, fig.width=6, fig.cap="Sequence logo with column heights proportional to information content."---- seqLogo(p) ## ----seqLogo2, fig.height=4, fig.width=6, fig.cap="Sequence logo with uniform column heights."---- seqLogo(p, ic.scale=FALSE) ## ----seqLogo3, fig.height=4, fig.width=6, fig.cap="Sequence logo with user specified colors."---- seqLogo(p, fill=c(A="#4daf4a", C="#377eb8", G="#ffd92f", T="#e41a1c"), ic.scale=FALSE) ## ----seqLogo4, fig.height=4, fig.width=6, fig.cap="RNA Sequence logo."-------- r <- makePWM(m, alphabet="RNA") seqLogo(r, ic.scale=FALSE) ## ----session-info------------------------------------------------------------- sessionInfo()