R: Zscore on three strains of Prochlorococcus marinus

prochlo {seqinr} | R Documentation

## 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)

### 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.
http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214

`citation("seqinr")`

### See Also

`zscore`

### Examples

    #
    # 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)
      }

[Package seqinr version 3.4-5 Index]