ggseg.formats (version 0.0.1)

atlas_manipulation: Manipulate brain atlas regions and views

Description

Functions for modifying brain atlas objects. These cover three areas:

Usage

atlas_region_remove(atlas, pattern, match_on = c("region", "label"))
atlas_region_contextual(atlas, pattern, match_on = c("region", "label"))
atlas_region_rename(atlas, pattern, replacement)
atlas_region_keep(atlas, pattern, match_on = c("region", "label"))
atlas_core_add(atlas, data, by = "region")
atlas_view_remove(atlas, views)
atlas_view_keep(atlas, views)
atlas_view_remove_region(
  atlas,
  pattern,
  match_on = c("label", "region"),
  views = NULL
)
atlas_view_remove_small(atlas, min_area, views = NULL)
atlas_view_gather(atlas, gap = 0.15)
atlas_view_reorder(atlas, order, gap = 0.15)

Value

Modified ggseg_atlas object

Arguments

atlas

A ggseg_atlas object

pattern

Character pattern to match. Uses grepl(..., ignore.case = TRUE).

match_on

Column to match against: "region" or "label".

replacement

For atlas_region_rename(): replacement string or function.

data

For atlas_core_add(): data.frame with metadata to join.

by

For atlas_core_add(): column(s) to join by. Default "region".

views

For view functions: character vector of view names or patterns. Multiple values collapsed with "|" for matching.

min_area

For atlas_view_remove_small(): minimum polygon area to keep. Context geometries are never removed.

gap

Proportional gap between views (default 0.15 = 15% of max width).

order

For atlas_view_reorder(): character vector of desired view order. Unspecified views appended at end.

Functions

• atlas_region_contextual(): Keep geometry for visual context but remove from core, palette, and 3D data. Context geometries render grey and don't appear in legends.

• atlas_region_rename(): Rename regions matching a pattern. Only affects the region column, not label. If replacement is a function, it receives matched names and returns new names.

• atlas_region_keep(): Keep only matching regions. Non-matching regions are removed from core, palette, and 3D data but sf geometry is preserved for surface continuity.

• atlas_core_add(): Join additional metadata columns to atlas core.

• atlas_view_remove(): Remove views matching pattern from sf data.

• atlas_view_keep(): Keep only views matching pattern.

• atlas_view_remove_region(): Remove specific region geometry from sf data only. Core, palette, and 3D data are unchanged.

• atlas_view_remove_small(): Remove region geometries below a minimum area threshold. Context geometries (labels not in core) are never removed. Optionally scope to specific views.

• atlas_view_gather(): Reposition remaining views to close gaps after view removal.

• atlas_view_reorder(): Reorder views and reposition. Views not in order are appended at end.

Details

Region manipulation modifies which regions are active in the atlas:

• atlas_region_remove(): completely remove regions

• atlas_region_contextual(): keep geometry but remove from core/palette

• atlas_region_rename(): rename regions in core

• atlas_region_keep(): keep only matching regions

View manipulation modifies the 2D sf geometry data:

• atlas_view_remove(): remove entire views

• atlas_view_keep(): keep only matching views

• atlas_view_remove_region(): remove specific region geometry from sf

• atlas_view_remove_small(): remove small polygon fragments

• atlas_view_gather(): reposition views to close gaps

• atlas_view_reorder(): change view order

Core manipulation modifies atlas metadata:

• atlas_core_add(): join additional metadata columns

Examples

dk() |>
  atlas_region_remove("bankssts") |>
  atlas_region_keep("frontal", match_on = "region")