# A group way to plot network structure based on similar vertex will be grouped together, while dissimilar nodes/vertex will depart from each others.

### Description

This function is for plotting different graphs into a same map with different colors, line styles and so on. The method for seperating the nodes in the two-dimensional spaces is the non-dimensional scaling technique, which can take the similarity matrices of the nodes as the input and generate the positions of the nodes in the space.

### Usage

1 |

### Arguments

`gemat` |
standard graph square matrix |

`groups` |
must be a list, each list element has the species that belong to a same group. |

`type` |
if type="both", the node similarity is calculated based on the the vertex similarity from the inward/outward links for each pair of nodes. if type="in", the node similarity is calculated based on the the vertex similarity from the inward links for each pair of nodes. if type="out", the node similarity is calculated based on the the vertex similarity from the outward links for each pair of nodes. |

`metric` |
node similarity methods, currently supporting two basic similarity indices: "jaccard" and "sorensen". |

`addlabels` |
if you want to label each node/vertex, set it's status as TRUE; default is FALSE |

`scaled` |
if you want to the links showing relative weights, set it's status as TRUE; default is FALSE links with larger weights will have thicker line width, vice versa. |

`pch` |
this pch is for nodes/vertex |

`bg` |
bg is for nodes/vertex filled background colors, will function when pch=21:25. |

`pcex` |
pcex is for nodes/vertex size |

`pcol` |
pcol is for nodes/vertex color |

`lty` |
lty is the line style for the links |

`lcol` |
lcol is the line color for the links |

`tfont` |
tfont is the font size for the labels of the nodes |

`tcol` |
tcol is the color for the labels of the nodes |

### Author(s)

Youhua Chen <haydi@126.com>

### References

Chen Y (2012) loop: an R package for performing decomposition of weighted directed graphs, food web analysis and flexible network plotting. Submitted.

### See Also

`fplot.foodweb`

,
`groupplot.foodweb`

,
`gplot`

,
`gplot1`

,

### Examples

1 2 3 4 5 6 | ```
mat=matrix(c(0,5,3,7,0,5,0,8,0,4,3,8,0,1,6,7,0,1,0,2,0,4,6,2,0),5,5)
glist<-list(c1=c(1:5),c2=c(1,3),c3=c(3,4,5))
pch=c(21,21,21) #length of the parameter vector should be identical to the number of species groups
bg=c(1,2,3)
lcol=c(8,2,4)
groupplot(gemat=mat,groups=glist,pch=pch,lcol=lcol,bg=bg) #other parameters are set in default
``` |