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Plot Density

Source: R/plot.R
plotDensity.Rd

Creates dot/line plots showing log2-transformed landmark fuzzy densities per sample. Unlike plotTradPerc() which plots cell percentages at the cluster/celltype level, this function plots landmark-level densities Useful for inspecting distributions and paired/longitudinal patterns at the landmark resolution.

Usage

plotDensity(x, ...)

# S3 method for class 'TDRObj'
plotDensity(
  x,
  .x.split = colnames(x = .tdr.obj@metadata)[1],
  .pop = NULL,
  .pop.from = "clustering",
  .subject.id = NULL,
  .color.by = NULL,
  .x.space.scaler = 0.25,
  .height = 1.5,
  .cat.feature.color = Color.Palette[1, 1:5],
  .seed = 123,
  .orientation = "wide",
  ...
)

Arguments

x

A TDRObj, Seurat, SingleCellExperiment, or HDF5AnnData (anndataR) object processed through get.map().

...

Additional arguments passed to methods.

.x.split

Character specifying metadata column for x-axis grouping (default first column).

.pop

Character vector of population names to plot. If NULL, plots all landmarks. If specified, plots only landmarks belonging to that population (from .pop.from).

.pop.from

Character: "clustering" (default) or "celltyping" - which grouping to use for filtering landmarks when .pop is specified.

.subject.id

Character metadata column for connecting paired samples with lines (e.g., "Subject"). Default NULL.

.color.by

Character metadata column for coloring points. Default NULL (all black).

.x.space.scaler

Numeric x-axis width scaling (default 0.25 inches per group).

.height

Numeric plot height in inches (default 1.5).

.cat.feature.color

Character vector of colors (default Color.Palette[1,1:5]).

.seed

Integer random seed for jitter (default 123).

.orientation

Character: "wide" (default) or "square" faceting.

Value

A ggplot object showing log2-transformed landmark densities.

See also

plotTradPerc, plotTradStats

Examples

if (FALSE) { # \dontrun{
# Basic density plot
plotDensity(lm.cells, .pop = "B.cells")

# With paired subject lines
plotDensity(lm.cells, 
              .pop = "B.cells",
              .subject.id = "MouseID",
              .color.by = "Treatment")
} # }