plot.dotprops | R Documentation |
plot.dotprops
plots a 2D projection of a
dotprops
format object
plot.neuron
plots a 2D projection of a neuron
## S3 method for class '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 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,
...
)
x |
a neuron to plot. |
scalevecs |
Factor by which to scale unit vectors (numeric, default: 1.0) |
alpharange |
Restrict plotting to points with |
col |
the color in which to draw the lines between nodes. |
PlotPoints, 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
|
asp |
the |
add |
Whether the plot should be superimposed on one already present
(default: |
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
|
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
|
... |
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 |
PointAlpha |
the value of alpha to use in plotting the nodes. |
lwd |
line width relative to the default (default=1). |
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.
list of plotted points (invisibly)
plot3d.neuron
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)
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