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Plot Marker DE Results

Source: R/plot.R
plotMarkerDE.Rd

Visualizes marker identification results from get.pbDE(.mode = "marker") as a colored heatmap showing log fold changes with significance overlays. Results are stored in .tdr.obj$markerDE[[.model.name]][[.comparison.name]].

Usage

plotMarkerDE(x, ...)

# S3 method for class 'TDRObj'
plotMarkerDE(
  x,
  .de.obj = NULL,
  .model.name = "default",
  .comparison.name = NULL,
  .coefs = NULL,
  .order.by = "none",
  .markers = .tdr.obj@config$markers,
  .q = 0.1,
  .row.space.scaler = 0.2,
  .col.space.scaler = 0.065,
  .label.substr.rm = "",
  ...
)

Arguments

x

A TDRObj, Seurat, SingleCellExperiment, or HDF5AnnData (anndataR) object with marker results from get.pbDE(.mode = "marker").

...

Additional arguments passed to methods.

.de.obj

Optional: Direct DE results object for backward compatibility. If NULL, fetches from .tdr.obj$markerDE[[.model.name]][[.comparison.name]].

.model.name

Character identifying the model (default "default").

.comparison.name

Character identifying the comparison (e.g., "cluster.1_vs_all"). Required if .de.obj is NULL.

.coefs

Character vector of coefficient names to plot. Default includes "(Intercept)" and ".id1" to show overall expression and group-specific enrichment.

.order.by

Source for marker ordering: "clustering" or "celltyping".

.markers

Features to include (default: all markers from .order.by).

.q

Numeric FDR threshold for significance markers (default 0.1).

.row.space.scaler

Numeric row height scaling (default 0.2).

.col.space.scaler

Numeric column width scaling (default 0.065).

.label.substr.rm

Character pattern to remove from coefficient labels.

Value

A ggplot heatmap showing log fold changes per feature and coefficient.

Details

The plot shows:

  • Fill color: Log fold change (blue = lower in .id1, red = higher in .id1)

  • Point size: -log10(adjusted p-value)

  • Asterisk overlay: Features passing the q-value threshold

For marker analysis, the key coefficient is typically ".id1" which represents the difference between group 1 and group 2 (or all other landmarks).

See also

get.pbDE, plotPbDE

Examples

if (FALSE) { # \dontrun{
# After running get.pbDE in marker mode
lm.cells <- get.pbDE(lm.cells, .mode = "marker", .id = "cluster.3",
                     .result.name = "cluster3_markers")

# Visualize marker results
plotMarkerDE(lm.cells, .comparison.name = "cluster3_markers",
             .coefs = c("(Intercept)", ".id1"))
} # }