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Plot Traditional Percentages

Source: R/plot.R
plotTradPerc.Rd

Creates dot/line plots showing cell percentages per sample for specific populations. Useful for visually inspecting distribution of cell abundances across conditions and identifying paired/longitudinal patterns. Complements statistical test results from plotTradStats().

Usage

plotTradPerc(x, ...)

# S3 method for class 'TDRObj'
plotTradPerc(
  x,
  .x.split = colnames(x = .tdr.obj@metadata)[1],
  .x.split.subset = NULL,
  .pop = NULL,
  .pop.from = "clustering",
  .order.pop = FALSE,
  .line.by = NULL,
  .dodge.by = NULL,
  .x.space.scaler = 0.25,
  .height = 1.5,
  .cat.feature.color = Color.Palette[1, 1:5],
  .seed = 123,
  .orientation = "wide",
  .log2.y = FALSE,
  ...
)

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. Defaults to first column.

.x.split.subset

Optional character vector to subset .x.split categories. Default NULL.

.pop

Character vector of population names to plot. If NULL, plots all populations from .pop.from.

.pop.from

Character: "clustering" (default) or "celltyping" - which grouping to plot.

.order.pop

Logical whether to order populations based on dendrogram order (default FALSE).

.line.by

Character metadata column for connecting paired samples with lines (e.g., "Subject" for longitudinal data). Default NULL (no lines).

.dodge.by

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

.x.space.scaler

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

.height

Numeric plot height in inches (default 1.5).

.cat.feature.color

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

.seed

Integer random seed for x-axis jitter (default 123).

.orientation

Character: "wide" (default, all populations in one row) or "square" (facet grid).

.log2.y

Logical whether to log2-transform y-axis percentages (default FALSE).

Value

A ggplot object showing cell percentages with optional paired connections.

Details

This function visualizes the raw cell percentages used in traditional DA testing. Points show individual samples, and lines (if .line.by specified) connect repeated measures from the same subject/mouse. Useful for:

  • Inspecting data distribution before statistical testing

  • Identifying outliers or batch effects

  • Visualizing paired/longitudinal designs

  • Confirming significant results have biological meaning

See also

plotTradStats, get.lm

Examples

if (FALSE) { # \dontrun{
# After mapping
lm.cells <- setup.tdr.obj(.cells = .cells, .meta = .meta) |>
  get.landmarks() |>
  get.graph() |>
  get.map()

# Plot CD4 T cells across conditions
plotTradPerc(lm.cells, .pop = "CD4.T.cells", .x.split = "Condition")

# Paired design with subject lines
plotTradPerc(lm.cells, 
             .pop = "CD4.T.cells",
             .line.by = "Subject",
             .dodge.by = "Timepoint")
} # }