plotA: Plot an interaction matrix.

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Plot an interaction matrix.

Description

By default, the interaction strengths are set to -1 or 1. Negative values are plotted in red, positive in green. If scale.weight is true, the interaction strengths are scaled to lie in the range of [-1,1]. The option original suppresses any modification of the interaction strengths. If interaction strengths are scaled or the original ones are used, the method ggplot is recommended, since it adds a color legend. Alternatively, the interaction matrix can also be visualized as a directed network with method network. In this case, the igraph network object is returned, to allow for manual adjustment of the layout with igraph's tkplot function. Method network recognizes separate taxon name columns in unmerged taxon matrices. Method ggplot requires ggplot2 and reshape2.

Usage

plotA(A, method = "image", header = "", scale.weight = FALSE,
  original = FALSE, setNAToZero = FALSE, pos.link.color = "green",
  neg.link.color = "red", removeOrphans = TRUE, removeLoops = FALSE,
  returnNetwork = FALSE)

Arguments

A	interaction matrix
method	image, ggplot or network (ggplot requires ggplot2 and reshape2, image is therefore default), image and ggplot will plot the matrix, network will plot the network with igraph
header	the title of the plot (does not apply to method network)
scale.weight	scale interaction strengths between -1 and 1 (does not apply to method network)
original	plot original values (does not apply to method network)
setNAToZero	set missing values to zeros
pos.link.color	color of positive edges
neg.link.color	color of negative edges
removeOrphans	remove orphan nodes (method network)
removeLoops	remove loops (method network)
returnNetwork	return the network for manual adjustment with tkplot (method network)

Examples

plotA(generateA(20,c=0.1))

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.