PlotPG: Plot data and principal graph(s)

Description Usage Arguments

Description

Plot data and principal graph(s)

Usage

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PlotPG(X, TargetPG, BootPG = NULL, PGCol = "", PlotProjections = "none",
  GroupsLab = NULL, PointViz = "points", Main = "", p.alpha = 0.3,
  PointSize = NULL, NodeLabels = NULL, LabMult = 1, Do_PCA = TRUE,
  DimToPlot = c(1, 2), VizMode = c("Target", "Boot"))

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

BootPG

A list of principal graphs that will be considered as bostrapped curves

PGCol

string, the label to be used for the main principal graph

PlotProjections

string, the plotting mode for the node projection on the principal graph. It can be "none" (no projections will be plotted), "onNodes" (the projections will indicate how points are associated to nodes), and "onEdges" (the projections will indicate how points are projected on edges or nodes of the graph)

GroupsLab

factor or numeric vector. A vector indicating either a category or a numeric value associted with each data point

PointViz

string, the modality to show points. It can be 'points' (data will be represented a dot) or 'density' (the data will be represented by a field)

Main

string, the title of the plot

p.alpha

numeric between 0 and 1, the alpha value of the points. Lower values will prodeuce more transparet points

PointSize

numeric vector, a vector indicating the size to be associted with each node of the graph. If NA points will have size 0.

NodeLabels

string vector, a vector indicating the label to be associted with each node of the graph

LabMult

numeric, a multiplier controlling the size of node labels

Do_PCA

bolean, should the node of the principal graph be used to derive principal component projections and rotate the space? If TRUE the plots will use the "EpG PC" as dimensions, if FALSE, the original dimensions will be used.

DimToPlot

a integer vector specifing the PCs (if Do_PCA=TRUE) or dimension (if Do_PCA=FALSE) to plot. All the combination will be considered, so, for example, if DimToPlot = 1:3, three plot will be produced.

VizMode

vector of string, describing the ElPiGraphs to visualize. Any combination of "Target" and "Boot".


Albluca/ElPiGraph.R documentation built on May 28, 2019, 11:02 a.m.