CCA/RDA plot for the rows of a
TreeSummarizedExperiment
object. The reduced dimension can be produced with runRDA
and gets stored in the reducedDim
slot of the experiment object. The panel implements plotRDA
to generate the plot.
The RDAPlot(...) constructor creates an instance of a RDAPlot class,
where any slot and its value can be passed to ... as a named argument.
The following slots control the thresholds used in the visualization:
add.ellipse, a string specifying ellipse layout (filled, coloured or absent).
colour_by, a string specifying the parameter to color by.
add.vectors, a logical indicating if vectors should appear in the plot.
vec.text, a logical indicating if text should be encased in a box.
confidence.level, a numeric between 0 and 1 to adjust confidence level.
ellipse.alpha, a numeric between 0 and 1 t o adjust ellipse opacity.
ellipse.linewidth, a numeric specifying the size of ellipses.
ellipse.linetype, a numeric specifying the style of ellipses.
vec.size, a numeric specifying the size of vectors.
vec.colour, a string specifying the colour of vectors.
vec.linetype, a numeric specifying the style of vector lines.
arrow.size, a numeric specifying the size of arrows.
label.colour, a string specifying the colour of text and labels.
label.size, a numeric specifying the size of text and labels.
add.significance, a logical indicating if variance and p-value
should appear in the labels.
add.expl.var, a logical indicating if variance should appear
on the coordinate axes.
In addition, this class inherits all slots from its parent Panel class.
# Import TreeSE
library(mia)
data("enterotype", package = "mia")
tse <- enterotype
# Run RDA and store results into TreeSE
tse <- runRDA(tse,
formula = assay ~ ClinicalStatus + Gender + Age,
FUN = vegan::vegdist,
distance = "bray",
na.action = na.exclude)
# Store panel into object
panel <- RDAPlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "dimred" "add.ellipse" "colour_by" "vec.text"
#> [5] "add.vectors" "ellipse.alpha"
# Launch iSEE with custom initial panel
if (interactive()) {
iSEE(tse, initial = c(panel))
}