addLink {combi} | R Documentation |
Add a link on a compositional plot
addLink(DIplot, links, Views, samples, variable = NULL, Dims = c(1, 2), addLabel = FALSE, labPos = NULL, projColour = "grey", latentSize = 0.25)
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 |
A ggplot object with the links added
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))