fsbrain (version 0.5.5)

coloredmesh.plot.colorbar.separate: Draw colorbar for coloredmeshes in separate 2D plot.

Description

Draw a colorbar for the coloredmeshes to a separate 2D plot. Due to the suboptimal handling of colorbar drawing in the three-dimensional multi-panel views, it is often desirable to plot the colorbar in a separate window, export it from there and then manually add it to the final plot version in some image manipulation software like Inkscape. If you need more control over the colormap than offered by this function (e.g., setting the color value for NA values or making a symmetric colormap to ensure that the zero point for divergent colormaps is a neutral color), you should write custom code, and the return value from this function will come in handy to do that.

Usage

coloredmesh.plot.colorbar.separate(
  coloredmeshes,
  show = FALSE,
  image.plot_extra_options = list(horizontal = FALSE, legend.cex = 1.8, legend.width = 2,
    legend.mar = 12, axis.args = list(cex.axis = 5)),
  png_options = list(filename = "fsbrain_cbar.png", width = 1400, height = 1400, bg =
    "#FFFFFF00"),
  silent = FALSE,
  trim_png = TRUE,
  log_breaks = FALSE
)

Value

named list, entries: 'output_img_path': character string, the path to the output file, or NULL.

Arguments

coloredmeshes

list of coloredmeshes. A coloredmesh is a named list as returned by the `coloredmesh.from` functions. It has the entries 'mesh' of type tmesh3d, a 'col', which is a color specification for such a mesh. The `vis*` functions (like vis.subject.morph.native) all return a list of coloredmeshes.

show

logical, Whether to open the resulting plot. Defaults to `TRUE`.

image.plot_extra_options

named list of extra optins to pass to image.plot. This can be used to add a legend to the colorbar, rotate the colorbar, or whatever. The options "legend_only", "zlim", and "col" are computed and set for you by this function, so there is no need to pass these. Your list will be merged with the internal options, so you could overwrite named arguments if needed.

png_options

Options to pass to png, see the docs of that function for details. Allow you to save the plot as a png bitmap image. Example: png_options = list("filename"="fsbrain_cbar.png", "width"=800). Defaults to NULL, which will not save anything.

silent

logical, whether to suppress messages. Defaults to `FALSE`.

trim_png

logical, whether to trim the output PNG image using image magick, i.e., remove everything but the foreground. Ignored unless an output PNG image is actually written (see 'png_options') and the 'magick' package is installed.

log_breaks

logical, scalar int, or vector of ints. Whether to use log10 scale for plotting the cbar. If logical and TRUE, uses log scale with default number (=5) ticks auto-computed from the data. If a single integer N, uses N ticks auto-computed from the data instead. If a numeric vector, uses the supplied values in the vector as ticks, note that they must be on a `log(data)` scale. If the 'makecmap_options' stored in the passed 'coloredmeshes' contain a 'base' value of 10, log 10 is assumed (with the default 5 ticks), even if this parameter is left at its default value, logical FALSE.

See Also

Other colorbar functions: combine.colorbar.with.brainview.animation(), combine.colorbar.with.brainview.image()

Examples

if (FALSE) {
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   coloredmeshes = vis.subject.morph.native(subjects_dir, 'subject1',
    'thickness', 'lh', views=c('t4'));
   coloredmesh.plot.colorbar.separate(coloredmeshes);

   # Or plot a colorbar with a label:
   coloredmesh.plot.colorbar.separate(coloredmeshes,
    image.plot_extra_options = list("legend.lab"="Thickness [mm]",
    horizontal=TRUE, legend.cex=1.5, legend.line=-3));
}