nat (version 1.8.24)

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

Description

Plot a 2D projection of a neuron

Usage

# S3 method for 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,
  ...
)

Value

list of plotted points (invisibly)

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.

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)