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Plot UMAP Visualization for Trajectory Analysis

plot_umap2.Rd

Creates UMAP visualizations optimized for trajectory analysis, with support for continuous color mapping and overlay comparisons.

Usage

plot_umap2(x, ...)

# Default S3 method
plot_umap2(
  x,
  dims = c("UMAP1", "UMAP2"),
  color.by = ".time",
  split.by = "label",
  order.by = "day_post_hatch",
  pt.size = 1.2,
  alpha_range = c(0.1, 0.5),
  ncol = NULL,
  title = NULL,
  overlay_mode = FALSE,
  base_label = NULL,
  compare_labels = NULL,
  base_color = "steelblue",
  compare_color = "orangered",
  ...
)

# S3 method for class 'Sap'
plot_umap2(
  x,
  segment_type = c("motifs", "syllables", "bouts", "segments"),
  data_type = c("feat.embeds", "traj.embeds"),
  dims = c("UMAP1", "UMAP2"),
  color.by = ".time",
  split.by = "label",
  order.by = "day_post_hatch",
  pt.size = 1.2,
  alpha_range = c(0.1, 0.5),
  ncol = NULL,
  title = NULL,
  overlay_mode = FALSE,
  base_label = NULL,
  compare_labels = NULL,
  base_color = "steelblue",
  compare_color = "orangered",
  verbose = TRUE,
  ...
)

Arguments

x

An object to visualize, either a data frame or SAP object

...

Additional arguments passed to specific methods

dims

UMAP dimensions to plot (default: c("UMAP1", "UMAP2"))

color.by

Column for continuous color mapping (default: ".time")

split.by

Column for faceting (default: "label")

order.by

Column for ordering facets (default: "day_post_hatch")

pt.size

Point size (default: 1.2)

alpha_range

Range for alpha transparency (default: c(0.1, 0.5))

ncol

Number of columns in layout

title

Plot title

overlay_mode

Whether to create overlay comparisons (default: FALSE)

base_label

Base label for overlay comparison

compare_labels

Labels to compare against base

base_color

Color for base label (default: "steelblue")

compare_color

Color for comparison labels (default: "orangered")

segment_type

For SAP objects: Type of segments ('motifs', 'syllables', 'bouts', 'segments')

data_type

For SAP objects: Type of embedding data ('feat.embeds', 'traj.embeds')

verbose

For SAP objects: Whether to print progress messages

Value

For default method: A ggplot object For SAP objects: Updated SAP object with plot as side effect

Details

Supports two visualization modes:

  • Standard mode: Continuous color mapping for trajectory visualization

  • Overlay mode: Direct comparison between trajectory patterns

Examples

if (FALSE) { # \dontrun{
# Basic trajectory plot
plot_umap2(traj_df, color.by = ".time")

# Overlay comparison plot
plot_umap2(traj_df,
           overlay_mode = TRUE,
           base_label = "a",
           compare_labels = c("b", "c"))

# Plot motif trajectories from SAP object
plot_umap2(sap_obj,
           segment_type = "motifs",
           data_type = "traj.embeds",
           color.by = ".time")

# Compare trajectories between labels
plot_umap2(sap_obj,
           segment_type = "motifs",
           data_type = "traj.embeds",
           overlay_mode = TRUE,
           base_label = "pre")
} # }