addLink: Add a link on a compositional plot

In combi: Compositional omics model based visual integration

Description

Add a link on a compositional plot

Usage

addLink(DIplot, links, Views, samples, variable = NULL, Dims = c(1, 2),
  addLabel = FALSE, labPos = NULL, projColour = "grey",
  latentSize = 0.25)

Arguments

DIplot	A list with ggplot object where the links are to be added, and data frames with coordinates (obtained by setting plot(..., returnCoords = TRUE))
links	A matrix containing either feature names (two column matrix) or approximate coordinates (four column matrix)
Views	Indices or names of the views for which the links should be added
samples	Sample names or approximate sample coordinates
variable	Name of variable in environmental gradient for which link should be plotted
Dims	vector of length 2 referring to the model dimensions
addLabel	A boolean, should arrow with label be plotted?
labPos	The position of the label, as a numeric vector of length 2
projColour	The colour of the projection, as character string
latentSize	Size of the line from the origin to the latent variable dot

Value

A ggplot object with the links added

Examples

data(Zhang)

#Unconstrained
microMetaboInt = combi(
list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
logTransformGaussian = FALSE, verbose = TRUE)

load(system.file("extdata", "zhangFits.RData", package = "combi"))
Plot = plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
 returnCoords = TRUE)
addLink(Plot, links = cbind("OTU0565b3","OTUa14fb5"), Views = 1,
 samples = c(1,1))

combi documentation built on Nov. 8, 2020, 5:34 p.m.