### R code from vignette source 'R4RNA.Rnw' ################################################### ### code chunk number 1: R4RNA.Rnw:40-54 ################################################### library(R4RNA) message("TRANSAT prediction in helix format") transat_file <- system.file("extdata", "helix.txt", package = "R4RNA") transat <- readHelix(transat_file) message("RFAM structure in dot bracket format") known_file <- system.file("extdata", "vienna.txt", package = "R4RNA") known <- readVienna(known_file) message("Work with basepairs instead of helices for more flexibility") message("Breaks all helices into helices of length 1") transat <- expandHelix(transat) known <- expandHelix(known) ################################################### ### code chunk number 2: R4RNA.Rnw:63-65 ################################################### plotHelix(known, line = TRUE, arrow = TRUE) mtext("Known Structure", side = 3, line = -2, adj = 0) ################################################### ### code chunk number 3: R4RNA.Rnw:73-76 ################################################### plotDoubleHelix(transat, known, line = TRUE, arrow = TRUE) mtext("TRANSAT\nPredicted\nStructure", side = 3, line = -5, adj = 0) mtext("Known Structure", side = 1, line = -2, adj = 0) ################################################### ### code chunk number 4: R4RNA.Rnw:84-86 ################################################### message("Filter out helices above a certain p-value") transat <- transat[which(transat$value <= 1e-3), ] ################################################### ### code chunk number 5: R4RNA.Rnw:92-100 ################################################### message("Assign colour to basepairs according to p-value") transat$col <- col <- colourByValue(transat, log = TRUE) message("Coloured encoded in 'col' column of transat structure") plotDoubleHelix(transat, known, line = TRUE, arrow = TRUE) legend("topright", legend = attr(col, "legend"), fill = attr(col, "fill"), inset = 0.05, bty = "n", border = NA, cex = 0.75, title = "TRANSAT P-values") ################################################### ### code chunk number 6: R4RNA.Rnw:112-113 ################################################### plotOverlapHelix(transat, known, line = TRUE, arrow = TRUE, scale = FALSE) ################################################### ### code chunk number 7: R4RNA.Rnw:130-137 ################################################### message("Multiple sequence alignment of interest") library(Biostrings) fasta_file <- system.file("extdata", "fasta.txt", package = "R4RNA") fasta <- as.character(readBStringSet(fasta_file)) message("Plot covariance in alignment") plotCovariance(fasta, known, cex = 0.5) ################################################### ### code chunk number 8: R4RNA.Rnw:147-148 ################################################### plotCovariance(fasta, transat, cex = 0.5, conflict.col = "grey") ################################################### ### code chunk number 9: R4RNA.Rnw:158-162 ################################################### col <- colourByCovariation(known, fasta, get = TRUE) plotCovariance(fasta, col, grid = TRUE, legend = FALSE) legend("topright", legend = attr(col, "legend"), fill = attr(col, "fill"), inset = 0.1, bty = "n", border = NA, cex = 0.37, title = "Covariation") ################################################### ### code chunk number 10: R4RNA.Rnw:168-173 ################################################### custom_colours <- c("green", "blue", "cyan", "red", "black", "grey") plotCovariance(fasta, col <- colourByConservation(known, fasta, get = TRUE), palette = custom_colours, cex = 0.5) legend("topright", legend = attr(col, "legend"), fill = attr(col, "fill"), inset = 0.15, bty = "n", border = NA, cex = 0.75, title = "Conservation") ################################################### ### code chunk number 11: R4RNA.Rnw:178-182 ################################################### col <- colourByCanonical(known, fasta, custom_colours, get = TRUE) plotCovariance(fasta, col, base.colour = TRUE, cex = 0.5) legend("topright", legend = attr(col, "legend"), fill = attr(col, "fill"), inset = 0.15, bty = "n", border = NA, cex = 0.75, title = "% Canonical") ################################################### ### code chunk number 12: R4RNA.Rnw:187-189 ################################################### col <- colourByUnknottedGroups(known, c("red", "blue"), get = TRUE) plotCovariance(fasta, col, base.colour = TRUE, legend = FALSE, species = 23, grid = TRUE, text = TRUE, text.cex = 0.2, cex = 0.5) ################################################### ### code chunk number 13: R4RNA.Rnw:197-199 ################################################### toLatex(sessionInfo())