R: Graphical representation for nucleotide skews in prokaryotic...

draw.oriloc {seqinr} | R Documentation

## Graphical representation for nucleotide skews in prokaryotic chromosomes.

### Description

Graphical representation for nucleotide skews in prokaryotic chromosomes.

### Usage

    draw.oriloc(ori, main = "Title",
      xlab = "Map position in Kb",
      ylab = "Cumulated combined skew in Kb", las = 1, las.right = 3,
      ta.mtext = "Cumul. T-A skew", ta.col = "pink", ta.lwd = 1,
      cg.mtext = "Cumul. C-G skew", cg.col = "lightblue", cg.lwd = 1,
      cds.mtext = "Cumul. CDS skew", cds.col = "lightgreen", cds.lwd = 1,
      sk.col = "black", sk.lwd = 2,
      add.grid = TRUE, ...)

### Arguments

`ori` | A data frame obtained with the `oriloc` function.
`main` | The main title of the plot.
`xlab` | The x-axis title.
`ylab` | The y-axis title.
`las` | The style of axis labels for the bottom and left axes.
`las.right` | The style of axis labels for the right axis.
`ta.mtext` | The marginal legend for the TA skew.
`ta.col` | The color for the TA skew.
`ta.lwd` | The line width for the TA skew.
`cg.mtext` | The marginal legend for the CG skew.
`cg.col` | The color for the CG skew.
`cg.lwd` | The line width for the CG skew.
`cds.mtext` | The marginal legend for the CDS skew.
`cds.col` | The color for the CDS skew.
`cds.lwd` | The line width for the CDS skew.
`sk.col` | The color for the cumulated combined skew.
`sk.lwd` | The line width for the cumulated combined skew.
`add.grid` | Logical, if `TRUE` a vertical grid is added to the plot.
`...` | Further arguments are passed to the function `plot`.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

`oriloc`, `rearranged.oriloc`, `extract.breakpoints`

### Examples

    ## Not run:  # need internet connection
    #
    # Example with Chlamydia trachomatis complete genome
    #
      ori <- oriloc()
      draw.oriloc(ori)
    #
    # The same, using more options from function draw.oriloc()
    #
    draw.oriloc(ori,
      main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome),
      ta.mtext = "TA skew", ta.col = "red",
      cg.mtext = "CG skew", cg.col = "blue",
      cds.mtext = "CDS skew", cds.col = "seagreen",
      add.grid = FALSE)

    ## End(Not run)

[Package seqinr version 3.4-5 Index]