draw.oriloc: Graphical representation for nucleotide skews in prokaryotic...

In seqinr: Biological Sequences Retrieval and Analysis

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)

seqinr documentation built on March 31, 2023, 3:05 p.m.