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)

Jean R. Lobry

References

citation("seqinr")

See Also

oriloc, rearranged.oriloc, extract.breakpoints

Examples

#
# 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)

Worked out examples



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