plot.neurocdf: Plot neuro-netcdf data

In kkholst/neurocdf: Various utilities for handling neuroimaging data

Description

Plot elements from neuro-netcdf data

Usage

  ## S3 method for class 'neurocdf'
 plot(x, slice, mm, plane = 3,
    roi = NULL, col = gray.colors(255),
    roi.col = lava:::Col(rev(rainbow(15, start = 0, end = 0.69)), 0.5),
    roi.range, colorbar = TRUE, new = TRUE, overlay.img,
    overlay = NULL, overlay.var = "SubjectImage",
    overlay.col = rainbow(64, start = 0, end = 0.69),
    overlay.zlim, realworld = TRUE, upsample = FALSE, ...)

Arguments

x	Neuro netCDF filename
slice	Slice number (not needed if mm is given)
mm	Slice given in real world coordinates mm (MNI)
plane	Coordinate (valid values: 1,2,3,x,y,z,median,sagittal,coronal,frontal,axial,transverse)
roi	Optional ROI from atlas to plot
col	Color of Template
roi.col	Color of ROI
roi.range	range of values in which to distribute roi.col
colorbar	if TRUE a horizontal colorbar (see colorbar) is added to the plot
new	Add new plot (default TRUE)
overlay.img	Image to overlay
overlay	Either a vector specifying the position of the overlay in the netCDF variable specified by overlay.group, or a matrix with columns of 1. coordinates and a column of 2. coordinates and optional a third column of values (defaults to 1)
overlay.var	netCDF variable from which to extract overlay
overlay.col	Color of overlay image
overlay.zlim	Range of z
realworld	Real-world coordinates
upsample	if TRUE image is upsampled (factor 2) and filtered to enhance resolution
...	Additional arguments to lower level functions

Author(s)

Klaus K. Holst

kkholst/neurocdf documentation built on May 20, 2019, 10:59 a.m.