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

Description Usage Arguments Value Note See Also Examples

View source: R/brainview_magick.R

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.

Usage

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vis.export.from.coloredmeshes(
  coloredmeshes,
  colorbar_legend = NULL,
  img_only = TRUE,
  horizontal = TRUE,
  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,
  ...
)

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

horizontal

logical, whether to plot the colorbar horizontally (TRUE) or vertically (FALSE). Pass 'NULL' to force no colorbar at all.

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.

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.

Note

Note that your screen resolution has to be high enough to generate the final image in the requested resolution, see the 'fsbrain FAQ' vignette for details and solutions if you run into trouble.

See Also

This function should not be used anymore, it will be deprecated soon. Please use the export function instead.

Examples

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## Not run: 
    rand_data = rnorm(327684, 5, 1.5);
    cm = vis.data.on.fsaverage(morph_data_both=rand_data,
      rglactions=list('no_vis'=T));
    vis.export.from.coloredmeshes(cm, colorbar_legend='Random data',
      output_img="~/fsbrain_arranged.png");

## End(Not run)

fsbrain documentation built on Sept. 16, 2021, 5:07 p.m.