Hierarchical tree for the columns of a
TreeSummarizedExperiment
object. The tree represents the sample hierarchy of the study and gets stored
in the colTree slot of the
experiment object. The panel implements plotColTree
to generate the plot.
The ColumnTreePlot(...) constructor creates an instance of a ColumnTreePlot
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 <- ColumnTreePlot()
# 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))
}