batch_plot: Batch plot timetrees from a directory of tree files

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Batch plot timetrees from a directory of tree files

Description

Batch plot timetrees from a directory of tree files

Usage

batch_plot(
  input_dir,
  output_dir,
  pattern = "*.tre",
  format = "pdf",
  width = 14,
  height = 10,
  overwrite = "ask",
  ignore_malformed = FALSE,
  ...
)

Arguments

input_dir	Input directory containing tree files
output_dir	Output directory for plots
pattern	File matching pattern (glob format, e.g., "*.tre")
format	Output format: "pdf", "png", "tiff", "svg", "eps" (default "pdf")
width	Output width in inches (default 14)
height	Output height in inches (default 10)
overwrite	Overwrite mode: "ask" (default), "force", or "no-clobber"
ignore_malformed	Logical. If TRUE, malformed tree inputs are skipped (with a warning) instead of aborting the whole batch, aligned with the CLI's --ignore_malformed flag. Default: FALSE.
...	Additional arguments passed to plot_timetree()

Value

Invisibly returns list of success/failure status

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.