Composite abundance profile of all features in a
TreeSummarizedExperiment
object. The panel implements plotAbundance
to generate the plot.
The AbundancePlot(...) constructor creates an instance of an
AbundancePlot 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:
rank, a string specifying the taxonomic rank to visualize.
use_relative, a logical indicating if the relative values should be calculated.
add_legend, a logical indicating if the color legend should appear.
In addition, this class inherits all slots from its parent Panel class.
# Import TreeSE
library(mia)
data("Tengeler2020", package = "mia")
tse <- Tengeler2020
# Store panel into object
panel <- AbundancePlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "rank" "use_relative" "add_legend"
#> [4] "order_sample_by_row" "order_sample" "decreasing"
# Launch iSEE with custom initial panel
if (interactive()) {
iSEE(tse, initial = c(panel))
}