plot.gmdp {GMD}R Documentation

Plot function for class gmdp

Description

Plot Function for Class gmdp

Usage

## S3 method for class 'gmdp'
plot(x, labels = NULL, colors = NULL, main,
  ylab = "Fraction", xlab = "Position", xlim = NULL, type = NULL,
  if.text.gmd = TRUE, if.text.gap = TRUE, ...)

Arguments

x

an object of class gmdp.

labels

a string vector of the same length of x$labels, giving the names of the numeric vectors in x.

colors

the colors of the discrete distributions. See help("plot.mhist", package="GMD").

main

an overall title for the plot.

ylab

a title for the y axis. See help("plot.mhist", package="GMD").

xlab

a title for the x axis. See help("plot.mhist", package="GMD").

xlim

numeric vectors of length 2, giving the x coordinates ranges.

type

type of plot, as in help("plot", package="graphics").

if.text.gmd

logical, indicating whether GM-Distance is reported in the subtitle.

if.text.gap

logical, indicating whether gap is reported in the subtitle.

...

arguments to be passed to methods. See help("plot.mhist", package="GMD").

Details

Plot Function for Class gmdp

References

See help(GMD)

See Also

gmdp

Examples

require("GMD") # load library
data(cage)     # load data

## measure pairwise distance
x <- gmdp(cage[["Pfkfb3 (T02R00AEC2D8)"]],cage[["Csf1 (T03R0672174D)"]])
print(x)                     # print a brief version by default
print(x, mode="full")  # print a full version by default

## show alignment
plot(x,labels=c("Pfkfb3","Csf1"),beside=FALSE)

## show another alignment
plot(gmdp(cage[["Hig1 (T09R0743763C)"]],cage[["Cd72 (T04R028B8BC9)"]]),
     labels=c("Hig1 (T09R0743763C)","Cd72 (T04R028B8BC9)"),
     beside=FALSE)
[Package GMD version 0.3.3 Index]