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mincPlotSliceSeries.Rd
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mincPlotSliceSeries.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/minc_vis2D.R
\name{mincPlotSliceSeries}
\alias{mincPlotSliceSeries}
\title{MINC Slice Series}
\usage{
mincPlotSliceSeries(
anatomy,
statistics = NULL,
dimension = 2,
mfrow = c(4, 5),
low = NULL,
high = NULL,
anatLow = NULL,
anatHigh = NULL,
col = heat.colors(255),
anatCol = gray.colors(255, start = 0),
begin = 1,
end = (dim(anatomy)[dimension] - 1),
symmetric = FALSE,
legend = NULL,
locator = !is.null(legend),
plottitle = NULL,
indicatorLevels = NULL,
discreteStats = FALSE,
legendHeight = 0.5
)
}
\arguments{
\item{anatomy}{A minc array of the anatomy volume to plot}
\item{statistics}{optional statistics or label file to overlay on anatomy slices}
\item{dimension}{integer denoting which dimension to slice across}
\item{mfrow}{A 2 element vector of the form c(rows, columns) indicating
the number and position of slices to draw - slices are added by rows}
\item{low}{the minimum statistic to plot, taken from histogram if not supplied
and not \code{discreteStats}, otherwise the minimum statistic}
\item{high}{the maximum statistic to plot, taken from histogram if not supplied
and not \code{discreteStats}, otherwise the maximum statistic}
\item{anatLow}{the minimum anatomy intensity to plot}
\item{anatHigh}{the maximum antomy intensity to plot}
\item{col}{colours for statistics or for the anatomy if statistics are not passed}
\item{anatCol}{colours for the}
\item{begin}{the first slice to plot, defaults to 1}
\item{end}{the last slice to plot, defaults to the last slice}
\item{symmetric}{whether the statistics are symmetric (such as for t-statistics)}
\item{legend}{an optional string to name the legend, indicating desire for a legend
(or not)}
\item{locator}{whether or not to draw the locator, defaults to whether or not
you requested a legend}
\item{plottitle}{the title of the plot if desired}
\item{indicatorLevels}{numeric vector indicating where to draw slice lines on the
locator, defaults to every slice}
\item{discreteStats}{Whether stats are discrete values and should should not have
their range taken from their histogram if unsupplied.}
\item{legendHeight}{What vertical fraction of the figure should the legend occupy}
}
\description{
Plot a series of slices through a minc volume
on a given dimension. Optionally superimpose statistics, and or include a locator
contour to show where slices are.
}
\details{
You can get a fuller tutorial on how to use the visualization tools by executing
the following command:
\code{file.show(system.file("doc/visualizationTutorial.html", package="RMINC"))}
On certain systems the slices are plotted with a reflected y-axis. To fix this
configure \code{options(RMINC_flip_image = TRUE)}
}
\examples{
\dontrun{
mincPlotSliceSeries(mincArray(anatVol), # the anatomical volume
mincArray(vs, "tvalue-SexM"), # pull out one column of the stats
anatLow=700, anatHigh=1400, # set anatomy thresholds
low=2.5, high=10, # set stats thresholds
symmetric=T, # show separate upper and lower
begin=25, end=-25 , # remove slices from both sides
legend="t-statistics")
}
}