plotCCA: Plot RDA or CCA object

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

Plot RDA or CCA object

Description

plotRDA and plotCCA create an RDA/CCA plot starting from the output of CCA and RDA functions, two common methods for supervised ordination of microbiome data.

Usage

plotCCA(x, ...)

## S4 method for signature 'SingleCellExperiment'
plotCCA(x, dimred, ...)

## S4 method for signature 'matrix'
plotCCA(x, ...)

plotRDA(x, ...)

## S4 method for signature 'SingleCellExperiment'
plotRDA(
  x,
  dimred,
  add.ellipse = TRUE,
  ellipse.alpha = 0.2,
  ellipse.linewidth = 0.1,
  ellipse.linetype = 1,
  confidence.level = 0.95,
  vec.size = 0.5,
  vec.color = vec.colour,
  vec.colour = "black",
  vec.linetype = 1,
  arrow.size = 0.25,
  label.color = label.colour,
  label.colour = "black",
  label.size = 4,
  vec.text = TRUE,
  repel.labels = TRUE,
  sep.group = "—",
  repl.underscore = " ",
  add.significance = TRUE,
  add.expl.var = TRUE,
  add.vectors = TRUE,
  parse.labels = TRUE,
  ...
)

## S4 method for signature 'matrix'
plotRDA(x, ...)

Arguments

x	a TreeSummarizedExperiment or a matrix of weights. The latter is returned as output from getRDA.
...	additional parameters for plotting, inherited from plotReducedDim, geom_label and geom_label_repel.
dimred	Character scalar or integer scalar. Determines the reduced dimension to plot. This is the output of addRDA and resides in reducedDim(tse, dimred).
add.ellipse	One of c(TRUE, FALSE, "fill", "colour", "color"), indicating whether ellipses should be present, absent, filled or colored. (default: ellipse.fill = TRUE)
ellipse.alpha	Numeric scalar. Between 0 and 1. Adjusts the opacity of ellipses. (Default: 0.2)
ellipse.linewidth	Numeric scalar. Specifies the size of ellipses. (Default: 0.1)
ellipse.linetype	Integer scalar. Specifies the style of ellipses. (Default: 1)
confidence.level	Numeric scalar. Between 0 and 1. Adjusts confidence level. (Default: 0.95)
vec.size	Numeric scalar. Specifies the size of vectors. (Default: 0.5)
vec.color	Alias for vec.colour.
vec.colour	Character scalar. Specifies the colour of vectors. (Default: "black")
vec.linetype	Integer scalar. Specifies the style of vector lines. (Default: 1)
arrow.size	Numeric scalar. Specifies the size of arrows. (defaults: arrow.size = 0.25)
label.color	Alias for label.colour.
label.colour	Character scalar. Specifies the colour of text and labels. (Default: "black")
label.size	Numeric scalar. Specifies the size of text and labels. (Default: 4)
vec.text	Logical scalar. Should text instead of labels be used to label vectors. (Default: TRUE)
repel.labels	Logical scalar. Should labels be repelled. (Default: TRUE)
sep.group	Character scalar. Specifies the separator used in the labels. (Default: "\U2014")
repl.underscore	Character scalar. Used to replace underscores in the labels. (Default: " ")
add.significance	Logical scalar. Should explained variance and p-value appear in the labels. (Default: TRUE)
add.expl.var	Logical scalar. Should explained variance appear on the coordinate axes. (Default: TRUE)
add.vectors	Logical scalar. Should vectors appear in the plot. (Default: TRUE)
parse.labels	Logical scalar. Should labels be parsed. (Default: TRUE)

Details

plotRDA and plotCCA create an RDA/CCA plot starting from the output of CCA and RDA functions, two common methods for supervised ordination of microbiome data. Either a TreeSummarizedExperiment or a matrix object is supported as input. When the input is a TreeSummarizedExperiment, this should contain the output of addRDA in the reducedDim slot and the argument dimred needs to be defined. When the input is a matrix, this should be returned as output from getRDA. However, the first method is recommended because it provides the option to adjust aesthetics to the colData variables through the arguments inherited from plotReducedDim.

Value

A ggplot2 object

Examples

# Load dataset
library(miaViz)
data("enterotype", package = "mia")
tse <- enterotype
 
# Run RDA and store results into TreeSE
tse <- addRDA(tse,
              formula = assay ~ ClinicalStatus + Gender + Age,
              FUN = vegan::vegdist,
              distance = "bray",
              na.action = na.exclude)
               
# Create RDA plot coloured by variable
plotRDA(tse, "RDA",
        colour.by = "ClinicalStatus")
 
# Create RDA plot with empty ellipses
plotRDA(tse, "RDA",
        colour.by = "ClinicalStatus",
        add.ellipse = "colour")
 
# Create RDA plot with text encased in labels
plotRDA(tse, "RDA",
        colour.by = "ClinicalStatus",
        vec.text = FALSE)
 
# Create RDA plot without repelling text
plotRDA(tse, "RDA",
        colour.by = "ClinicalStatus",
        repel.labels = FALSE)
 
# Create RDA plot without vectors
plotRDA(tse, "RDA",
        colour.by = "ClinicalStatus",
        add.vectors = FALSE)
 
# Calculate RDA as a separate object
rda_mat <- getRDA(tse,
                  formula = assay ~ ClinicalStatus + Gender + Age,
                  FUN = vegan::vegdist,
                  distance = "bray",
                  na.action = na.exclude)
 
# Create RDA plot from RDA matrix
plotRDA(rda_mat)

microbiome/miaViz documentation built on Aug. 13, 2024, 8:57 p.m.