Plot multi-round logFC trends for monotonic gene groups

This function visualizes log fold-change (logFC) trajectories of genes classified by multi-round monotonic time-course patterns (e.g. Up1, Down2). Individual gene trajectories are shown as semi-transparent lines, while the group-level mean trajectory is overlaid for each pattern.

Usage

plot_FC_trend(se, group_by = "condition")

Arguments

se

A SummarizedExperiment object containing concentration-based expression data and log fold-change values.

group_by

Character string specifying the column in colData(se) used to define experimental conditions. Default is "condition".

Value

A ggplot object showing logFC trajectories faceted by gene trend group.

Details

Genes are grouped according to their assigned trend group, and facets are ordered by round index, with Up* and Down* displayed as paired groups within each round.

The function performs the following steps:

1. Convert the SummarizedExperiment object to a gene-level data frame using se2conc().

2. Retain only genes classified as Up or Down.

3. Reshape logFC values into long format for plotting.

4. Reorder gene groups as paired rounds (Up1, Down1, Up2, Down2, ...).

5. Plot individual gene trajectories and overlay group-level mean trends.

Facet labels include the number of genes (n) in each group.

See also

classify_timecourse_by_round, se2conc, ggplot

Examples

if (FALSE) { # \dontrun{
p <- plot_FC_trend(se, group_by = "condition")
print(p)
} # }