plot-methods: Plot methods for CorMut package

In CorMut: Detect the correlated mutations based on selection pressure

Description

Plot implement plot methods for ckaksCodon,ckaksAA,miCodon, miAA and biCompare objects respectively. Plot visualize the mutation correlation among sites or amino mutations.

Methods

x = "ckaks"

Plot the results of ckaks object. The paramater "layout_reset" was provided to set the layout of the network. You can refer to "layout_ function" in igraph package to get the graph layouts

x = "MI"

Plot the results of MI object. The paramater "layout_reset" was provided to set the layout of the network. You can refer to "layout_ function" in igraph package to get the graph layouts

x = "JI"

Plot the results of JI object. The paramater "layout_reset" was provided to set the layout of the network. You can refer to "layout_ function" in igraph package to get the graph layouts

x = "biCompare"

Plot the results of biCompare object. The paramater "layout_reset" was provided to set the layout of the network. You can refer to "layout_ function" in igraph package to get the graph layouts

Author(s)

Zhenpeng Li

See Also

ckaksCodon,ckaksAA,miCodon,miAA,jiAA

Examples

examplefile=system.file("extdata","PI_treatment.aln",package="CorMut")
example=seqFormat(examplefile)
result=ckaksAA(example)
plot(result)

Example output

Loading required package: seqinr
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

CorMut documentation built on April 28, 2020, 7:09 p.m.