## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) CRANpkg <- function(pkg) { cran <- "https://cran.r-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function(pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } # Packages ------------------------------------------------------------------- library(ggmsa) library(ggplot2) ## ----eval = FALSE------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("ggmsa") ## ----results="hide", message=FALSE, warning=FALSE----------------------------- library(ggmsa) ## ----echo=FALSE, out.width='50%'---------------------------------------------- knitr::include_graphics("man/figures/workflow.png") ## ----warning=FALSE------------------------------------------------------------ available_msa() protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa") miRNA_sequences <- system.file("extdata", "seedSample.fa", package = "ggmsa") nt_sequences <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa") ## ----fig.height = 2, fig.width = 10, warning=FALSE---------------------------- ggmsa(protein_sequences, 300, 350, color = "Clustal", font = "DroidSansMono", char_width = 0.5, seq_name = TRUE ) ## ----warning=FALSE------------------------------------------------------------ available_colors() ## ----echo=FALSE, out.width = '50%'-------------------------------------------- knitr::include_graphics("man/figures/schemes.png") ## ----warning=FALSE------------------------------------------------------------ available_fonts() ## ----fig.height = 2.5, fig.width = 11, warning = FALSE, message = FALSE------- ggmsa(protein_sequences, 221, 280, seq_name = TRUE, char_width = 0.5) + geom_seqlogo(color = "Chemistry_AA") + geom_msaBar() ## ----echo=FALSE, results='asis', warning=FALSE, message=FALSE----------------- library(kableExtra) x <- "geom_seqlogo()\tgeometric layer\tautomatically generated sequence logos for a MSA\n geom_GC()\tannotation module\tshows GC content with bubble chart\n geom_seed()\tannotation module\thighlights seed region on miRNA sequences\n geom_msaBar()\tannotation module\tshows sequences conservation by a bar chart\n geom_helix()\tannotation module\tdepicts RNA secondary structure as arc diagrams(need extra data)\n " xx <- strsplit(x, "\n\n")[[1]] y <- strsplit(xx, "\t") %>% do.call("rbind", .) y <- as.data.frame(y, stringsAsFactors = FALSE) colnames(y) <- c("Annotation modules", "Type", "Description") knitr::kable(y, align = "l", booktabs = TRUE, escape = TRUE) %>% kable_styling(latex_options = c("striped", "hold_position", "scale_down")) ## ----echo = FALSE------------------------------------------------------------- sessionInfo()