Hierarchical tree for the rows of a
TreeSummarizedExperiment
object. The tree can be produced with addTaxonomyTree
and gets stored in the rowTree
slot of the experiment object. The panel implements plotRowTree
to generate the plot.
The RowTreePlot(...) constructor creates an instance of a RowTreePlot
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 tree layout
add_legend, a logical indicating if color legend should appear.
edge_colour_by, a string specifying parameter to color lines by
when colour_parameters = "Edge".
edge_size_by, a string specifying parameter to size lines by
when size_parameters = "Edge".
tip_colour_by, a string specifying parameter to color tips by
when colour_parameters = "Tip".
tip_size_by, a string specifying parameter to size tips by
when size_parameters = "Tip".
tip_shape_by, a string specifying parameter to shape tips by
when shape_parameters = "Tip".
node_colour_by, a string specifying parameter to color nodes by
when colour_parameters = "Node".
node_size_by, a string specifying parameter to size nodes by
when size_parameters = "Node".
node_shape_by, a string specifying parameter to shape nodes by
when shape_parameters = "Node".
order_tree, a logical indicating if tree is ordered by
alphabetic order of taxonomic levels.
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 <- RowTreePlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "layout" "add_legend" "edge_colour_by" "tip_colour_by"
#> [5] "order_tree" "tip_size_by"
# Launch iSEE with custom initial panel
if (interactive()) {
iSEE(tse, initial = c(panel))
}