Visualizes single-cell gene expression trends along the Tocky Time axis. Accepts multiple genes and automatically generates a grid layout. Automatically detects Lineage_Bias from the mCanonicalTockyObj.
Usage
mPlotGeneDynamics(object, seurat_obj, features, ...)
# S4 method for class 'mCanonicalTockyObj'
mPlotGeneDynamics(
object,
seurat_obj,
features,
group_by = "Lineage_Bias",
span = 0.8,
jitter_amount = 0.2,
pt_alpha = 0.2,
m = 1.15,
ncol = 2
)Arguments
- object
An mCanonicalTockyObj.
- seurat_obj
Original Seurat object.
- features
Character vector of genes to plot.
- ...
Additional arguments passed to methods.
- group_by
Optional metadata column in Seurat or TockyData to color by. Defaults to "Lineage_Bias".
- span
Numeric. Smoothing span for LOESS (default 0.8).
- jitter_amount
Numeric. Amount of vertical jitter applied to expression values to reduce overplotting (default 0.2).
- pt_alpha
Numeric. Transparency level for the plotted cells, ranging from 0 (transparent) to 1 (opaque) (default 0.2).
- m
Numeric. Multiplier for the maximum y-axis limit to ensure curves and data points fit comfortably within the plot (default 1.15).
- ncol
Integer. Number of columns for the plot grid (default 2).