plotPieNet: Plot a graph with pie chart associated with each node

Description Usage Arguments

View source: R/plotting.R

Description

Plot a graph with pie chart associated with each node

Usage

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plotPieNet(X, TargetPG, GroupsLab = NULL, Nodes = NULL, Partition = NULL,
  TrimmingRadius = Inf, Graph = NULL, LayOut = "nicely",
  LayoutIter = 500, TreeRoot = numeric(), RootLevel = numeric(),
  distMeth = "manhattan", Main = "", ScaleFunction = sqrt,
  NodeSizeMult = 1, ColCat = NULL, Leg.cex = 1, Leg.pos = "bottom",
  Leg.horiz = TRUE, Arrow.size = 1, NodeLabels = NULL, LabSize = 1)

Arguments

X

numerical 2D matrix, the n-by-m matrix with the position of n m-dimensional points

TargetPG

the main principal graph to plot

GroupsLab

string factor, a vector indicating the category of each data point

Nodes

integer, the vector of nodes to plot. If NULL, all the nodes will be plotted.

Partition

A vector associating each point to a node of the ElPiGraph. If NULL (the default), this will be computed

TrimmingRadius

numeric, the trimming radius to use when associting points to nodes when Partition = NULL

Graph

a igraph object of the ElPiGraph, if NULL (the default) it will be computed by the function

LayOut

the global layout of yhe final network. It can be

  • 'tree', a tree

  • 'circle', a closed circle

  • 'circle_line', a line arranged as a circle

  • 'kk', a topology generated by the Kamada-Kawai layout algorithm

  • 'mds', a topology generated by multidimensional scaling on the node positions

  • 'fr', a topology generated by the Fruchterman-Reingold layout algorithm

  • 'nicely', the topology will be inferred by igraph

LayoutIter

numeric, the number of interation of the layout algorithm

TreeRoot

the id of the node to use as the root of the tree when LayOut = 'tree', multiple nodes are allowed.

RootLevel

numeric, the level of the root(s)

distMeth

the matric used to compute the distance if LayOut = 'mds'

Main

string, the title of the plot

ScaleFunction

function, a function used to scale the nuumber of points (sqrt by default)

NodeSizeMult

integer, an adjustment factor to control the size of the pies

ColCat

string vector, a vector of colors to associate to each category

Leg.cex

numeric, a value to adjust the size of the legend

Leg.pos

character, the position of the legend (see the help of the legend function)

Leg.horiz

boolean, should the legend be plotted in horizontal

Arrow.size

numeric, the size of the arrow

NodeLabels

character vector, the names of the nodes

LabSize

numeric, the size of the node labels


Albluca/ElPiGraph.R documentation built on June 10, 2018, 5:22 p.m.