prochlo: Zscore on three strains of Prochlorococcus marinus

Description

This dataset contains the zscores computed with the codon model on all CDS from 3 strains of Procholorococcus marinus (as retrieved from Genome Reviews database on June 16, 2005)

Usage

data(prochlo)

Arguments

Format

List of three dataframes of the zscore of each of the 16 dinucleotides on each CDS retrieved from the specific strain.

BX548174: strain adapted to living at a depth of 5 meters (high levels of UV exposure) base model on each intergenic sequence
AE017126: strain adapted to living at a depth of 120 meters (low levels of UV exposure)
BX548175: strain adapted to living at a depth of 135 meters (low levels of UV exposure)

References

Palmeira, L., Guéguen, L. and Lobry JR. (2006) UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219.
https://academic.oup.com/mbe/article/23/11/2214/1335460

citation("seqinr")

Examples

Run this code

#
# Show the four YpY for the three ecotypes:
#
data(prochlo)
oneplot <- function(x){
  plot(density(prochlo$BX548174[, x]),
    ylim = c(0,0.4), xlim = c(-4,4), lty=3,
    main = paste(substr(x,1,1), "p", substr(x,2,2), " bias", sep = ""),
    xlab="",ylab="",las=1, type = "n")
  rect(-10,-1,-1.96,10, col = "yellow", border = "yellow")
  rect(1.96,-1,10,10, col = "yellow", border = "yellow")
  lines(density(prochlo$BX548174[, x]),lty=3)
  lines(density(prochlo$AE017126[, x]),lty=2)
  lines(density(prochlo$BX548175[, x]),lty=1)
  abline(v=c(-1.96,1.96),lty=5)
  box()
}
par(mfrow=c(2,2),mar=c(2,3,2,0.5) + 0.1)
oneplot("CT")
oneplot("TC")
oneplot("CC")
oneplot("TT")
#
# Show YpY biases with respect to light exposure
#
curdev <- getOption("device")
OK <- FALSE
devlist <- c("X11", "windows", "quartz") # interactive with width and height in inches
for(i in devlist){
  if(exists(i) && identical(get(i), curdev)){
    OK <- TRUE
    break
  }
}
if(OK){
  curdev(width = 18, height = 11)
  par(oma = c(0, 0, 3, 0), mfrow = c(1, 2), mar = c(5, 4, 0, 0), cex = 1.5)
  example(waterabs, ask = FALSE) #left figure

  par(mar = c(5, 0, 0, 2))
  plot(seq(-5, 3, by = 1), seq(0, 150, length = 9), col = "white", 
    ann = FALSE, axes = FALSE, xaxs = "i", yaxs = "i")
  axis(1, at = c(-1.96, 0, 1.96), labels = c(-1.96, 0, 1.96))
  lines(rep(-1.96, 2),c(0, 150),lty=2)
  lines(rep(1.96, 2), c(0, 150),lty=2)
  title(xlab = "zscore distribution", cex = 1.5, adj = 0.65)

  selcol <- c(6, 8, 14, 16)
  z5 <- prochlo$BX548174[, selcol]
  z120 <- prochlo$AE017126[, selcol]
  z135 <- prochlo$BX548175[, selcol]

  todo <- function(who, xx, col = "black", bottom, loupe){
  	dst <- density(who[, xx])
  	sel <- which(dst$x >= -3)
    	lines(dst$x[sel], dst$y[sel]*loupe + (bottom), col = col)
  }
  todo2 <- function(who, bottom, loupe){
    todo(who, "CC", "blue", bottom, loupe)
    todo(who, "CT", "red", bottom, loupe)
    todo(who, "TC", "green", bottom, loupe)
    todo(who, "TT", "black", bottom, loupe)
  }
  todo3 <- function(bottom, who, leg, loupe = 90){
    lines(c(-5,-3), c(150 - leg, bottom + 20))
    rect(-3,bottom,3,bottom+40)
    text(-2.6,bottom+38, paste(leg, "m"))
    todo2(who, bottom, loupe)
  }

  todo3(bottom = 110, who = z5, leg = 5)
  todo3(bottom = 50, who = z120, leg = 120)
  todo3(bottom = 5, who = z135, leg = 135)

  legend(-4.5,110,c('CpC','CpT','TpC','TpT'),lty=1,pt.cex=cex,
    col=c('blue','red','green','black'))

  mtext(expression(paste("Dinucleotide composition for three ", 
    italic("Prochlorococcus marinus")," ecotypes")), outer = TRUE, cex = 2, line = 1)
  }