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Plot Gene Expression Dynamics by Group (Fixed Color Mapping & Robust Limits)

Source: R/plotCanonicalTocky.R
plotGeneDynamics.Rd

Visualizes gene expression trends along the Gradient Tocky Time axis (0-90 degrees). Supports both data frame output from GradientTocky_Slerp and simple numeric vectors.

Usage

plotGeneDynamics(
  expression_data,
  gradient_res,
  gene,
  groups = NULL,
  group_cols = NULL,
  span = 0.8,
  jitter_amount = 0.2,
  pt_alpha = 0.2,
  m = 1.15
)

Arguments

expression_data

Sparse matrix or data frame (Genes x Cells).

gradient_res

Either the data frame returned by GradientTocky_Slerp OR a named numeric vector of angles.

gene

Character string. The gene symbol to plot.

groups

Optional Character or Factor vector defining cell groups (e.g., "WT", "KO").

group_cols

Optional vector of colors. Can be named (c("WT"="black")) or unnamed.

span

Numeric. Smoothing span for LOESS (default 0.8).

jitter_amount

Numeric. Amount of vertical jitter for points (default 0.2).

pt_alpha

Numeric. Transparency of single cell points (0-1).

m

Numeric. Magnification factor for y-max.