Animate a Deformetrica geodesic flow as a nat.ggplot GIF

A thin convenience wrapper around nat.ggplot::ggneuron_gif() (where the general "animate a sequence of nat objects to a GIF" machinery now lives). It renders a set of warping objects across the timepoints of a geodesic flow (as returned by deformetrica_shoot() with flow = TRUE) to a ping-pong GIF, each object in its own colour over an optional reference volume and static greyscale targets. Kept for convenience/back-compatibility; new code can call nat.ggplot::ggneuron_gif() directly.

Usage

ggplot_flow_gif(
  flows,
  cols = NULL,
  volume = NULL,
  volume_alpha = 0.12,
  volume_col = "grey80",
  targets = NULL,
  target_cols = NULL,
  target_alpha = 0.18,
  alpha = 0.6,
  rotation_matrix = NULL,
  points = NULL,
  point_cols = NULL,
  point_size = 3,
  point_alpha = 1,
  point_stroke = 0.8,
  file = NULL,
  width = 900,
  height = 800,
  delay = 0.14,
  dpi = 96
)

Arguments

flows: A named list; each element is the per-timepoint list of objects for one structure (all lists the same length). Colours are taken per structure.
cols: Named vector of colours (one per flows entry); recycled from a default palette if NULL.
volume: Optional fixed reference object drawn translucent under every frame (e.g. the target brain hull).
volume_alpha, target_alpha, alpha: Alphas for the reference volume, the target objects and the flow objects.
volume_col: Colour of the reference volume (default "grey80"; pass e.g. a light pink to render the brain hull as a soft envelope).
targets: Optional named list of fixed reference objects drawn translucent above the volume but below the flow (e.g. the matched target neuropils each warping object should land on). Static across frames.
target_cols: Named vector of colours for targets (one per entry); defaults to a transparent greyscale ramp so the coloured flow reads clearly on top.
rotation_matrix: Optional 4x4 view matrix (as nat.ggplot/rgl use).
points: Optional named list of point sets drawn as circles on top of the neurons - e.g. neuron root points / somata. Each entry is either a static N x 3 matrix or a per-timepoint list of matrices (circles that move with the warp), forwarded to nat.ggplot::ggneuron_gif().
point_cols: Named fill colours for points (one per entry).
point_size, point_alpha, point_stroke: Circle size, opacity and outline width for points.
file: Output GIF path. Frames are written next to it.
width, height, delay, dpi: GIF frame size (px), per-frame delay (s) and dpi.

Value

The GIF path if written (needs gifski, or falls back to magick), else the vector of frame PNGs.

Usage

Arguments

Value

See also