overlay: Add overlay slices

In Mouse-Imaging-Centre/MRIcrotome: Visualization Tools for 3D Volumes

Description

Adds overlay slices; usually used for statistics, but can be anything. Differs from anatomy in that the background is transparent.

Usage

overlay(ssm, volume, low = NULL, high = NULL, col = defaultCol(),
  symmetric = FALSE, rCol = defaultRCol(), alpha = NULL,
  underTransparent = TRUE, name = NULL, box = FALSE)

Arguments

ssm	The slice series info, usually passed along the pipe and specified by the user
volume	3D matrix representing the volume from which to obtain slices. Can be either numbers or hexadecimal colours
low	Lower end of colour scale. Can be NULL if volume is a matrix of hexadecimals. If symmetric=TRUE, then treat this as an absolute value (i.e. 2 would be >2 and < -2)
high	Upper end of colour scale.
col	The colour scale. See defaultCol for default.
symmetric	Whether the colour scale is symmetric.
rCol	The reverse colour scale. Used if symmetric=TRUE. See defaultRCol for default.
alpha	Value between 0 and 1, 0 being full transparent and 1 fully opaque.
underTransparent	Whether to make the under colour transparent. Defaults to TRUE.
name	Optional name.

Value

The slices series for continuation down the pipe.

Examples

## Not run: 
sliceSeries(nrow = 1, begin=200, end=300) %>%
  anatomy(anatVol, low=700, high=1400) %>%
  overlay(stats, low=2, high=6, symmetric = T) %>%
  legend("t-statistics") %>%
  draw()

## End(Not run)

Mouse-Imaging-Centre/MRIcrotome documentation built on Feb. 27, 2020, 1:31 p.m.