Nothing
#
# Genetic code table as in Text Books
#
tablecode <- function(numcode = 1, urn.rna = s2c("TCAG"), dia = FALSE,
latexfile = NULL, label = latexfile, size = "normalsize", caption = NULL,
preaa = rep("", 64), postaa = rep("", 64),
precodon = preaa, postcodon = postaa)
{
aa1 <- a()
aa3 <- aaa()
codename <- SEQINR.UTIL$CODES.NCBI[numcode, "ORGANISMES"]
urn <- s2c("tcag") # internal
#
# Make default caption for LaTeX table:
#
if( is.null(caption) ){
caption <- paste("\\caption{Genetic code number ",
numcode, ": ", codename, ".}", sep = "")
}
#
# As a LaTex table:
#
if( ! is.null(latexfile) ) {
Tfile <- file(latexfile, open = "w")
cat("\\begin{table}", file = Tfile, sep = "
")
cat("\\begin{center}", file = Tfile, sep = "
")
#
# Character size:
#
cat(paste("{\\", size, sep = ""), file = Tfile, sep = "
")
cat("\\begin{tabular}{*{13}{l}}", file = Tfile, sep = "
")
cat("\\hline", file = Tfile, sep = "
")
cat("\\\\", file = Tfile, sep = "
")
ncodon <- 1 # codon rank as in
#paste(paste(rep(s2c("tcag"), each = 16), s2c("tcag"), sep = ""), rep(s2c("tcag"), each = 4), sep = "")
for( i in 0:3 )
{
for( j in 0:3 )
{
for( k in 0:3 )
{
codon <- c(urn[i+1], urn[k+1], urn[j+1])
codon.urn <- paste(urn.rna[i+1], urn.rna[k+1], urn.rna[j+1], sep = "", collapse = "")
codon.urn <- paste(precodon[ncodon], codon.urn, postcodon[ncodon], sep = "")
aminoacid <- aa3[which(aa1 == translate(codon, numcode = numcode))]
aminoacid <- paste(preaa[ncodon], aminoacid, postaa[ncodon], sep = "")
cat(paste(codon.urn, aminoacid, " &", sep = " & "), file = Tfile, sep = "
")
ncodon <- ncodon + 1
}
cat("\\\\", file = Tfile, sep = "
")
}
cat("\\\\", file = Tfile, sep = "
")
}
cat("\\hline", file = Tfile, sep = "
")
cat("\\end{tabular}", file = Tfile, sep = "
")
#
# Caption:
#
cat(caption, file = Tfile, sep = "
")
#
# LaTeX label:
#
cat(paste("\\label{", label, "}", sep = ""), file = Tfile, sep = "
")
#
# End character size:
#
cat("}", file = Tfile, sep = "
")
cat("\\end{center}", file = Tfile, sep = "
")
cat("\\end{table}", file = Tfile, sep = "
")
close(Tfile)
return(invisible(NULL))
}
#
# END LATEX
#
if( dia )
{
op <- par(no.readonly = TRUE)
par(bg = "blue")
par(fg = "yellow")
par(col = "yellow")
par(col.axis = "yellow")
par(col.lab = "yellow")
par(col.main = "yellow")
par(col.sub = "yellow")
}
plot.new()
plot.window(xlim=c(0,100),ylim=c(0,100))
segments( 0, 102, 100, 102, lwd = 2)
segments( 0, 0, 100, 0, lwd = 2)
segments( 0, 97, 100, 97)
text(x=0, y = 98.5, font = 2, adj = c(0, 0),
lab = paste("Genetic code", numcode,":",codename))
urn <- c("t","c","a","g") # internal
for( i in 0:3 )
{
for( j in 0:3 )
{
for( k in 0:3 )
{
codon <- c(urn[i+1], urn[j+1], urn[k+1])
text( x = 100*j/4, y = 95 - 100*i/4 -5*k, adj = c(-0.5,1.5),
lab = urn.rna[i+1] )
text( x = 100*j/4 + 3, y = 95 - 100*i/4 -5*k, adj = c(-0.5,1.5),
lab = urn.rna[j+1] )
text( x = 100*j/4 + 6, y = 95 - 100*i/4 -5*k, adj = c(-0.5,1.5),
lab = urn.rna[k+1] )
aminoacid <- aa3[which(aa1 == translate(codon, numcode = numcode))]
text( x = 100*j/4 + 12, y = 95 - 100*i/4 -5*k, adj = c(-0.5,1.5),
lab = aminoacid )
}
}
}
if(dia)
par(op)
}
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