`plot.dotprops`

plots a 2D projection of a
`dotprops`

format object

`plot.neuron`

plots a 2D projection of a neuron

```
# S3 method for dotprops
plot(
x,
scalevecs = 1,
alpharange = NULL,
col = "black",
PlotPoints = FALSE,
PlotVectors = TRUE,
UseAlpha = FALSE,
asp = 1,
add = FALSE,
axes = TRUE,
tck = NA,
boundingbox = NULL,
xlim = NULL,
ylim = NULL,
soma = FALSE,
...
)
# 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,
...
)
```

- x
a neuron to plot.

- scalevecs
Factor by which to scale unit vectors (numeric, default: 1.0)

- alpharange
Restrict plotting to points with

`alpha`

values in this range to plot (default: null => all points). See`dotprops`

for definition of`alpha`

.- col
the color in which to draw the lines between nodes.

- PlotPoints
Whether to plot points and/or tangent vectors (logical, default: tangent vectors only)

- PlotVectors
Whether to plot points and/or tangent vectors (logical, default: tangent vectors only)

- UseAlpha
Whether to scale tangent vector length by the value of

`alpha`

- asp
the

`y/x`

aspect ratio, see`plot.window`

.- add
Whether the plot should be superimposed on one already present (default:

`FALSE`

).- axes
whether axes should be drawn.

- 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).

- 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)- xlim
limits for the horizontal axis (see also boundingbox)

- ylim
limits for the vertical axis (see also boundingbox)

- 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.- ...
additional arguments passed 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.

- PlotAxes
the axes for the plot.

- main
the title for the plot

- sub
sub title for the plot

- 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.- PointAlpha
the value of alpha to use in plotting the nodes.

- lwd
line width relative to the default (default=1).

list of plotted points (invisibly)

`plot.dotprops`

is limited in that 1) it cannot plot somata
directly (this is handled by `plot.neuronlist`

) and 2) it can
only plot a frontal (XY) view.

`plot.neuron`

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 modifying the AxisDirections argument.

Other neuron:
`neuron()`

,
`ngraph()`

,
`potential_synapses()`

,
`prune()`

,
`resample()`

,
`rootpoints()`

,
`spine()`

,
`subset.neuron()`

```
plot(kcs20[[1]], col='red')
# NB soma ignored
plot(kcs20[[1]], col='red', soma=TRUE)
plot(kcs20[1], col='red', soma=TRUE)
# 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)
```