Density abundance profile of single features in a
TreeSummarizedExperiment.
The panel implements plotAbundanceDensity
to generate the plot.
The AbundanceDensityPlot(...) constructor creates an instance of an
AbundanceDensityPlot class, where any slot and its value can be passed to
... as a named argument.
The following slots control the thresholds used in the visualisation:
layout, a string specifying abundance layout (jitter, density or points).
assay.type, a string specifying the assay to visualize.
n, a number indicating the number of top taxa to visualize.
flipped, a logical specifying if the axis should be switched.
order_descending, a string specifying the descending order.
In addition, this class inherits all slots from its parent Panel class.
# Import TreeSE
library(mia)
#> Loading required package: MultiAssayExperiment
#> Loading required package: TreeSummarizedExperiment
#> Loading required package: Biostrings
#> Loading required package: XVector
#>
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#>
#> strsplit
#> This is mia version 1.15.6
#> - Online documentation and vignettes: https://microbiome.github.io/mia/
#> - Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
data("Tengeler2020", package = "mia")
tse <- Tengeler2020
# Add relabundance assay
tse <- transformAssay(tse, method = "relabundance")
# Store panel into object
panel <- AbundanceDensityPlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "layout" "assay.type" "n" "dots_colour"
#> [5] "dots_colour_by" "add_legend"
# Launch iSEE with custom initial panel
if (interactive()) {
iSEE(tse, initial = c(panel))
}