Package 'sulcimap'

Clear sulcimap cached assets

Description

Clear sulcimap cached assets

Usage

clear_sulcimap_cache()

Value

Logical TRUE if cache removed or did not exist

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Lightweight assets for light example Unzips a tiny assets bundle and returns the directory path.

Description

Lightweight assets for light example Unzips a tiny assets bundle and returns the directory path.

Usage

get_assets_light()

Value

A character scalar: path to the unzipped assets directory.

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Path to sulcimap extracted asset directory

Description

Unzips the bundled assets into a cache (persistent for users, temporary under checks)

Usage

get_sulcimap_assets_dir()

Value

Character scalar: full path to the root of extracted assets

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Full path to a bundled PNG (after extraction)

Description

Full path to a bundled PNG (after extraction)

Usage

get_sulcus_image(name)

Arguments

name	Relative path inside the assets (e.g. "leftlat/S.C._left.png")

Value

Character scalar: full path

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List bundled PNGs (after extraction)

Description

List bundled PNGs (after extraction)

Usage

list_sulci_images()

Value

Character vector of relative PNG paths

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Plot sulcal measures on brain

Description

Generates composite brain figures (left/right lateral/medial) by mapping sulcal values.

Usage

plot_sulci(
  sulcus_values,
  palette = "gyr",
  value_range = NULL,
  save_dir = NULL,
  measure = c("all", "opening", "depth", "surface", "length"),
  show_colorbar = TRUE,
  caption = expression(-log[10](p)),
  ...
)

Arguments

sulcus_values	data.frame or path/to/csv Either (1) a two-column dataframe with Sulcus and Value, or (2) a path to a CSV file containing those columns. Sulcus must use BrainVISA-style tags (left/right, 4 types) and include all expected names. Missing sulcus should have Value = 0 (see README and data samples).
palette	character Color palette for mapping values and the colorbar. Options include "viridis", "magma", "plasma", "inferno", "cividis", "heat", "gyr".
value_range	numeric length-2 or NULL (default NULL) Controls the color scale. NULL: auto-scale from the min/max of the provided values. c(min, max): fix the scale across plots/conditions for comparability.
save_dir	character or NULL (default NULL) Directory where the plot image(s) are saved. If it does not exist, it will be created. Set to NULL to skip saving and only return the plot object.
measure	character What to plot: "all": generate all four measures in one figure. "opening", "depth", "surface", "length": generate a single-measure plot.
show_colorbar	logical Show or hide the color bar on the figure.
caption	character or expression Label displayed with the color bar. For math, use e.g. expression(-log[10](p)).
...	Advanced options: base_dir (path to assets), scale_width (magick scale, default "1000x"), file_prefix (default "sulci"), width_in, height_in (inches; defaults 14, 8), dpi (default 300).

Value

If save_dir = NULL, returns a ggplot (or patchwork) object representing the brain figure, which can be further modified and saved. If save_dir is not NULL, the plot image(s) are automatically saved in that directory and the function (invisibly) returns a character vector with the path(s) to the saved file(s).

Examples

# Minimal executable example using assets_light
ex <- data.frame(
  Sulcus = c("S.C._left.opening", "S.C._right.opening",
  "S.F.int._left.opening", "S.F.int._right.opening"),
  Value  = c(1, 0.5, 0.8, 0.4)
)
assets_light <- sulcimap::get_assets_light()
p <- plot_sulci(
  sulcus_values = ex,
  measure       = "opening",
  palette       = "gyr",
  show_colorbar = FALSE,
  base_dir      = assets_light,
  save_dir      = NULL
)
# p is a ggplot/patchwork object; printing it will draw the figure.


# Full example
# df should have columns: Sulcus (BrainVISA-style names with suffixes), Value
# plot_out <- plot_sulci(
#  sulcus_values = df,
#    palette       = "gyr",
#   value_range   = NULL,
#  save_dir      = NULL,
#    measure       = "opening",
#    show_colorbar = TRUE,
#    caption       = expression(-log[10](p))
# )

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