plot.neuron: Plot a 2D projection of a neuron

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Plot a 2D projection of a neuron

Description

Plot a 2D projection of a neuron

Usage

## S3 method for class 'neuron'
plot(
  x,
  WithLine = TRUE,
  WithNodes = TRUE,
  WithAllPoints = FALSE,
  WithText = FALSE,
  PlotSubTrees = TRUE,
  soma = FALSE,
  PlotAxes = c("XY", "YZ", "XZ", "ZY"),
  axes = TRUE,
  asp = 1,
  main = x$NeuronName,
  sub = NULL,
  xlim = NULL,
  ylim = NULL,
  AxisDirections = c(1, -1, 1),
  add = FALSE,
  col = NULL,
  PointAlpha = 1,
  tck = NA,
  lwd = par("lwd"),
  boundingbox = NULL,
  ...
)

Arguments

x	a neuron to plot.
WithLine	whether to plot lines for all segments in neuron.
WithNodes	whether points should only be drawn for nodes (branch/end points)
WithAllPoints	whether points should be drawn for all points in neuron.
WithText	whether to label plotted points with their id.
PlotSubTrees	Whether to plot all sub trees when the neuron is not fully connected.
soma	Whether to plot a circle at neuron's origin representing the soma. Either a logical value or a numeric indicating the radius (default FALSE). When soma=TRUE the radius is hard coded to 2.
PlotAxes	the axes for the plot.
axes	whether axes should be drawn.
asp	the y/x aspect ratio, see plot.window.
main	the title for the plot
sub	sub title for the plot
xlim	limits for the horizontal axis (see also boundingbox)
ylim	limits for the vertical axis (see also boundingbox)
AxisDirections	the directions for the axes. By default, R uses the bottom-left for the origin, whilst most graphics software uses the top-left. The default value of c(1, -1, 1) makes the produced plot consistent with the latter.
add	Whether the plot should be superimposed on one already present (default: FALSE).
col	the color in which to draw the lines between nodes.
PointAlpha	the value of alpha to use in plotting the nodes.
tck	length of tick mark as fraction of plotting region (negative number is outside graph, positive number is inside, 0 suppresses ticks, 1 creates gridlines).
lwd	line width relative to the default (default=1).
boundingbox	A 2 x 3 matrix (ideally of class boundingbox) that enables the plot axis limits to be set without worrying about axis selection or reversal (see details)
...	additional arguments passed to plot

Details

This functions sets the axis ranges based on the chosen PlotAxes and the range of the data in x. It is still possible to use PlotAxes in combination with a boundingbox, for example to set the range of a plot of a number of objects.

nat assumes the default axis convention used in biological imaging, where the origin of the y axis is the top rather than the bottom of the plot. This is achieved by reversing the y axis of the 2D plot when the second data axis is the Y axis of the 3D data. Other settings can be achieved by modfiying the AxisDirections argument.

Value

list of plotted points (invisibly)

See Also

plot3d.neuron

Other neuron: neuron(), ngraph(), potential_synapses(), prune(), resample(), rootpoints(), spine(), subset.neuron()

Examples

# Draw first example neuron
plot(Cell07PNs[[1]])
# Overlay second example neuron
plot(Cell07PNs[[2]], add=TRUE)
# Clear the current plot and draw the third neuron from a different view
plot(Cell07PNs[[3]], PlotAxes="YZ")
# Just plot the end points for the fourth example neuron
plot(Cell07PNs[[4]], WithNodes=FALSE)
# Plot with soma (of default radius)
plot(Cell07PNs[[4]], WithNodes=FALSE, soma=TRUE)
# Plot with soma of defined radius
plot(Cell07PNs[[4]], WithNodes=FALSE, soma=1.25)

nat documentation built on May 29, 2024, 10:36 a.m.