fsbrain (version 0.5.5)

export: Export high-quality brainview image with a colorbar.

Description

This function serves as an easy (but slightly inflexible) way to export a high-quality, tight-layout, colorbar figure to disk. If no colorbar is required, one can use vislayout.from.coloredmeshes instead. It is an alias for `vis.export.from.coloredmeshes` that requires less typing.

Usage

export(
  coloredmeshes,
  colorbar_legend = NULL,
  img_only = TRUE,
  draw_colorbar = "horizontal",
  horizontal = NULL,
  silent = TRUE,
  quality = 1L,
  output_img = "fsbrain_arranged.png",
  image.plot_extra_options = NULL,
  large_legend = TRUE,
  view_angles = get.view.angle.names(angle_set = "t4"),
  style = "default",
  grid_like = TRUE,
  background_color = "white",
  transparency_color = NULL,
  ...
)

Value

magick image instance or named list, depending on the value of 'img_only'. If the latter, the list contains the fields 'rev_vl', 'rev_cb', and 'rev_ex', which are the return values of the functions vislayout.from.coloredmeshes, coloredmesh.plot.colorbar.separate, and combine.colorbar.with.brainview.image, respectively.

Arguments

coloredmeshes

list of coloredmesh. A coloredmesh is a named list as returned by the `coloredmesh.from*` functions (like coloredmesh.from.morph.native). 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.

colorbar_legend

character string or NULL, the title for the colorbar.

img_only

logical, whether to return only the resulting image

draw_colorbar

logical or one of the character strings 'vertical' or 'horizontal', whether to draw a colorbar. Defaults to 'horizontal'.

horizontal

deprecated (since 0.5.0) and ignored, use parameter 'draw_colorbar' instead.

silent

logical, whether to suppress messages

quality

integer, an arbitrary quality. This is the resolution per tile before trimming, divided by 1000, in pixels. Example: 1L means 1000x1000 pixels per tile before trimming. Currently supported values: 1L..2L. Note that the resolution you can get is also limited by your screen resolution.

output_img

string, path to the output file. Defaults to "fsbrain_arranged.png"

image.plot_extra_options

named list, custom options for fields::image.plot. Overwrites those derived from the quality setting. If in doubt, leave this alone.

large_legend

logical, whether to plot extra large legend text, affects the font size of the colorbar_legend and the tick labels.

view_angles

list of strings. See get.view.angle.names for all valid strings.

style

the rendering style, see material3d or use a predefined style like 'default' or 'shiny'.

grid_like

logical, passed to vislayout.from.coloredmeshes.

background_color

hex color string (like '#FFFFFF'), the color to use for the background. Ignored if 'transparency_color' is not NULL. To get a transparent background, use 'transparency_color' instead of this parameter. WARNING: Do not use color names (like 'gray'), as their interpretation differs between rgl and image magick!

transparency_color

hex color string (like '#FFFFFF'), the temporary background color that will get mapped to transparency, or NULL if you do not want a transparent background. If used, it can be any color that does not occur in the foreground. Try '#FFFFFF' (white) or '#000000' (black) if in doubt. WARNING: Do not use color names (like 'gray'), as their interpretation differs between rgl and image magick!

...

extra arguments passed to vislayout.from.coloredmeshes.

Examples

if (FALSE) {
    rand_data = rnorm(327684, 5, 1.5);
    cm = vis.data.on.fsaverage(morph_data_both=rand_data,
      rglactions=list('no_vis'=T));
    export(cm, colorbar_legend='Random data',
      output_img="~/fsbrain_arranged.png");
}