addOrthProjection: This function adds orthogonal projections to a given plot

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

This function adds orthogonal projections to a given plot

Usage

addOrthProjection(
  RCMplot,
  sample = NULL,
  species = NULL,
  variable = NULL,
  Dims = c(1, 2),
  addLabel = FALSE,
  labPos = NULL
)

Arguments

RCMplot	the RCMplot object
sample, species, variable	names or approximate coordinates of sample, species or variable
Dims	The dimensions of the solutions that have been plotted
addLabel	a boolean, should the r-s-psi label be added?
labPos	the position of the label. Will be calculated if not provided

Value

a modified ggplot object that contains the geom_segment object that draws the projection

See Also

plot.RCM

Examples

data(Zeller)
require(phyloseq)
tmpPhy = prune_taxa(taxa_names(Zeller)[seq_len(100)],
prune_samples(sample_names(Zeller)[seq_len(50)], Zeller))
zellerRCM = RCM(tmpPhy, k = 2, round = TRUE)
zellerPlot = plot(zellerRCM, returnCoords = TRUE)
addOrthProjection(zellerPlot, species = c(-0.35,1.1), sample = c(1,1.2))

RCM documentation built on Nov. 8, 2020, 5:22 p.m.