Plot sample coordinates on the recovered state-transition axis (Stage 1 output)

Shows each layer's sample coordinates along the shared state-transition axis recovered by Stage 1. When the object carries a SubspaceGroundTruth (synthetic data), the angle between the recovered axis and the true axis is annotated.

Usage

plot_decomposition(std, colour_by = NULL, component = 1L)

Arguments

std

StateTransitionData with metadata()$stage1 present

colour_by

character column name in colData(std) to colour samples by, or NULL for unlabelled points (default NULL)

component

integer – which component column to plot from each layer's coordinate matrix (default 1L). Use plot_components() to inspect descriptive distributions; scientific selection requires the atlas/proposal and confirmation workflow.

Value

a ggplot object

Details

This is a descriptive display. It neither selects a component nor confirms biological separation.

Examples

std <- synthetic_control(n = 40L, p = 500L, K = 2L, signal = 30, seed = 1L)
ctor <- get_strategy("Decomposer", "hogsvd_averaged")
std2 <- suppressWarnings(decompose(ctor(), std))@value
plot_decomposition(std2)