Contribution of single features in a
TreeSummarizedExperiment
to the components of a target reduced dimension. The panel implements
plotLoadings to generate the plot.
The LoadingPlot(...) constructor creates an instance of an
LoadingPlot 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:
dimred, a string specifying the dimred to visualize.
layout, a string specifying abundance layout (barplot or heatmap).
ncomponents, a number indicating the number of components to visualize.
add.tree, a logical indicating whether the tree should be shown.
In addition, this class inherits all slots from its parent Panel class.
# Import libraries
library(mia)
library(scater)
#> Loading required package: scuttle
#> Loading required package: ggplot2
# Import TreeSE
data("Tengeler2020", package = "mia")
tse <- Tengeler2020
# Add relabundance assay
tse <- transformAssay(tse, method = "relabundance")
# Add reduced dimensions
tse <- runPCA(tse, assay.type = "relabundance")
#> Warning: more singular values/vectors requested than available
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
# Store panel into object
panel <- LoadingPlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "dimred" "layout" "ncomponents" "add.tree" "VersionInfo"
#> [6] "PanelId"
# Launch iSEE with custom initial panel
if (interactive()) {
iSEE(tse, initial = c(panel))
}