ColorMappedNeuroSurface: ColorMappedNeuroSurface

In bbuchsbaum/neurosurf: Data structures and visualization for surface-based neuroimaging data

ColorMappedNeuroSurface

Description

This function creates a ColorMappedNeuroSurface object, which represents a single set of data values associated with nodes on a surface geometry, with pre-defined color mapping parameters.

Usage

ColorMappedNeuroSurface(geometry, indices, data, cmap, irange, thresh)

Arguments

geometry	A SurfaceGeometry object representing the underlying surface structure.
indices	An integer vector specifying the indices of valid surface nodes.
data	A numeric vector of data values corresponding to the surface nodes.
cmap	A character vector defining the sequence of colors (e.g., hex codes) for the colormap.
irange	A numeric vector of length 2 specifying the minimum and maximum data values that map to the start and end of the 'cmap'.
thresh	A numeric vector of length 2 specifying the lower and upper thresholds. Values outside this range might be rendered differently (e.g., transparently, depending on the plotting function).

Details

This object bundles the surface geometry, data, and specific color mapping parameters ('cmap', 'irange', 'thresh'). This is useful for ensuring consistent visualization across different plots or for saving a predefined view. The actual application of the color map happens during rendering (e.g., when using 'plot()”).

Value

A new object of class ColorMappedNeuroSurface.

See Also

SurfaceGeometry, NeuroSurface

Examples

# Load a sample surface geometry
surf_file <- system.file("extdata", "std.8.lh.inflated.asc", package = "neurosurf")
surf_geom <- read_surf_geometry(surf_file)

# Get vertex count and generate some random data
n_verts <- nrow(coords(surf_geom))
set.seed(123)
vertex_data <- rnorm(n_verts)

# Define indices (all vertices in this case)
vertex_indices <- 1:n_verts

# Define color mapping parameters
my_cmap <- colorRampPalette(c("blue", "white", "red"))(256) # Blue-white-red colormap
my_irange <- c(-2, 2) # Map data values from -2 to 2 onto the colormap
my_thresh <- c(-1, 1) # Define thresholds (e.g., for transparency later)

# Create the ColorMappedNeuroSurface object
mapped_surf <- ColorMappedNeuroSurface(geometry = surf_geom,
                                       indices = vertex_indices,
                                       data = vertex_data,
                                       cmap = my_cmap,
                                       irange = my_irange,
                                       thresh = my_thresh)

# Print the object summary
print(mapped_surf)

# The object can now be plotted, and the plotting function will use
# the stored cmap, irange, and thresh parameters by default.
# plot(mapped_surf) # Requires rgl package

bbuchsbaum/neurosurf documentation built on June 10, 2025, 8:22 p.m.