## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----set-options, echo=FALSE, cache=FALSE----------------------------------------------------------------------------- options(width = 120) ## ----lib,warning=FALSE,message=FALSE---------------------------------------------------------------------------------- library(Biostrings) library(GenomAutomorphism) ## ----fasta, message=FALSE--------------------------------------------------------------------------------------------- data(covid_aln, package = "GenomAutomorphism") covid_aln ## ----int-------------------------------------------------------------------------------------------------------------- base2int("ACGT", group = "Z4", cube = "ACGT") ## ----int2------------------------------------------------------------------------------------------------------------- base2int("ACGT", group = "Z5", cube = "ACGT") ## ----url, message=FALSE----------------------------------------------------------------------------------------------- codons <- codon_coord( codon = covid_aln, cube = "ACGT", group = "Z64", chr = 1L, strand = "+", start = 1, end = 750) codons ## ----bp--------------------------------------------------------------------------------------------------------------- x0 <- c("ACG", "TGC") x1 <- DNAStringSet(x0) x1 ## ----bp_coord--------------------------------------------------------------------------------------------------------- x2 <- base_coord(x1, cube = "ACGT") x2 x2. <- base_coord(x1, cube = "TGCA") x2. ## ----bp_sum.---------------------------------------------------------------------------------------------------------- ## cube "ACGT" (x2$coord1 + x2$coord2) %% 4 ## cube "TGCA" (x2.$coord1 + x2.$coord2) %% 4 ## ----bp_sum----------------------------------------------------------------------------------------------------------- ## Codon ACG (x2$coord1 + x2.$coord1) %% 4 ## Codon TGC (x2$coord2 + x2.$coord2) %% 4 ## ----codons----------------------------------------------------------------------------------------------------------- ## cube ACGT x3 <- codon_coord(codon = x2, group = "Z64") x3 ## cube TGCA x3. <- codon_coord(codon = x2., group = "Z64") x3. ## ----bp_sum2---------------------------------------------------------------------------------------------------------- ## cube "ACGT" (as.numeric(x3$coord1) + as.numeric(x3$coord2)) %% 64 ## cube "TGCA" (as.numeric(x3.$coord1) + as.numeric(x3.$coord2)) %% 64 ## ----bp_sum3---------------------------------------------------------------------------------------------------------- ## Codon ACG (as.numeric(x3$coord1) + as.numeric(x3.$coord1)) %% 64 ## Codon TGC (as.numeric(x3$coord2) + as.numeric(x3.$coord2)) %% 64 ## ----aut-------------------------------------------------------------------------------------------------------------- autm <- automorphisms( seqs = covid_aln, group = "Z64", cube = c("ACGT", "TGCA"), cube_alt = c("CATG", "GTAC"), start = 1, end = 750, verbose = FALSE) autm ## ----range------------------------------------------------------------------------------------------------------------ aut_range <- automorphismByRanges(autm) aut_range ## ----aut_1, eval=FALSE------------------------------------------------------------------------------------------------ # ## Do not need to run it. # covid_autm <- automorphisms( # seq = covid_aln, # group = "Z64", # cube = c("ACGT", "TGCA"), # cube_alt = c("CATG", "GTAC"), # verbose = FALSE) ## ----dat-------------------------------------------------------------------------------------------------------------- data(covid_autm, package = "GenomAutomorphism") covid_autm ## ----range_2---------------------------------------------------------------------------------------------------------- aut_range <- automorphismByRanges(covid_autm) aut_range ## ----non-aut---------------------------------------------------------------------------------------------------------- idx = which(covid_autm$cube == "Trnl") covid_autm[ idx ] ## ----range_3---------------------------------------------------------------------------------------------------------- idx = which(aut_range$cube == "Trnl") aut_range[ idx ] ## ----indels----------------------------------------------------------------------------------------------------------- data.frame(aut_range[idx]) ## region width width(aut_range[ idx ]) ## ----barplot, fig.height = 5, fig.width = 6--------------------------------------------------------------------------- counts <- table(covid_autm$cube[ covid_autm$autm != 1 | is.na(covid_autm$autm) ]) par(family = "serif", cex = 0.9, font = 2, mar=c(4,6,4,4)) barplot(counts, main="Automorphism distribution", xlab="Genetic-code cube representation", ylab="Fixed mutational events", col=c("darkblue","red", "darkgreen"), border = NA, axes = FALSE, cex.lab = 2, cex.main = 1.5, cex.names = 2) axis(2, at = c(0, 200, 400, 600, 800), cex.axis = 1.5) mtext(side = 1,line = -1.5, at = c(0.7, 1.9, 3.1, 4.3, 5.5), text = paste0( counts ), cex = 1.4, col = c("white","yellow", "black")) ## ----autby------------------------------------------------------------------------------------------------------------ autby_coef <- automorphism_bycoef(covid_autm) autby_coef <- autby_coef[ autby_coef$autm != 1 & autby_coef$autm != -1 ] ## ----barplot_2, fig.height = 12, fig.width = 14----------------------------------------------------------------------- counts <- table(autby_coef$mut_type) counts <- sort(counts, decreasing = TRUE) count. <- counts[ counts > 2 ] par(family = "serif", cex.axis = 2, font = 2, las = 1, cex.main = 1.4, mar = c(6,2,4,4)) barplot(count., main="Automorphism distribution per Mutation type", col = colorRampPalette(c("red", "yellow", "blue"))(36), border = NA, axes = FALSE,las=2) axis(side = 2, cex.axis = 2, line = -1.8 ) ## ----ct--------------------------------------------------------------------------------------------------------------- counts ## ----conserved_regions------------------------------------------------------------------------------------------------ conserv <- conserved_regions(covid_autm) conserv ## ----uniq------------------------------------------------------------------------------------------------------------- conserv_unique <- conserved_regions(covid_autm, output = "unique") conserv_unique ## ----aut_2, eval=FALSE------------------------------------------------------------------------------------------------ # autm_z125 <- automorphisms( # seq = covid_aln, # group = "Z125", # cube = c("ACGT", "TGCA"), # cube_alt = c("CATG", "GTAC"), # verbose = FALSE) ## ----autm_z125-------------------------------------------------------------------------------------------------------- data(autm_z125, package = "GenomAutomorphism") autm_z125 ## ----range_4---------------------------------------------------------------------------------------------------------- aut_range_2 <- automorphismByRanges(autm_z125) aut_range_2 ## ----barplot_3, fig.height = 5, fig.width = 3------------------------------------------------------------------------- counts <- table(autm_z125$cube[ autm_z125$autm != 1 ]) par(family = "serif", cex = 1, font = 2) barplot(counts, main="Automorphism distribution", xlab="Genetic-code cube representation", ylab="Fixed mutational events", col=c("darkblue","red"), ylim = c(0, 1300), border = NA, axes = TRUE) mtext(side = 1,line = -2, at = c(0.7, 1.9, 3.1), text = paste0( counts ), cex = 1.4, col = c("white","red")) ## ----aut_3, eval=FALSE------------------------------------------------------------------------------------------------ # autm_3d <- automorphisms( # seq = covid_aln, # group = "Z5^3", # cube = c("ACGT", "TGCA"), # cube_alt = c("CATG", "GTAC"), # verbose = FALSE) ## ----autm_3d---------------------------------------------------------------------------------------------------------- data(autm_3d, package = "GenomAutomorphism") autm_3d ## ----autby_3---------------------------------------------------------------------------------------------------------- autby_coef_3d <- automorphism_bycoef(autm_3d) autby_coef_3d <- autby_coef_3d[ autby_coef_3d$autm != "1,1,1" ] autby_coef_3d ## ----conserved_regions_3---------------------------------------------------------------------------------------------- conserv <- conserved_regions(autm_3d) conserv ## ----barplot_4, fig.height = 5, fig.width = 3------------------------------------------------------------------------- counts <- table(autby_coef_3d$cube[ autby_coef_3d$autm != "1,1,1"]) par(family = "serif", cex = 1, font = 2, cex.main = 1) barplot(counts, main="Automorphism distribution", xlab="Genetic-code cube representation", ylab="Fixed mutational events", col=c("darkblue","red"), ylim = c(0, 1300), border = NA, axes = TRUE) mtext(side = 1,line = -2, at = c(0.7, 1.9), text = paste0( counts ), cex = 1.4, col = c("white")) ## ----sessionInfo, echo=FALSE------------------------------------------------------------------------------------------ sessionInfo()