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,
...
)
a neuron to plot.
Factor by which to scale unit vectors (numeric, default: 1.0)
Restrict plotting to points with alpha
values in
this range to plot (default: null => all points). See
dotprops
for definition of alpha
.
the color in which to draw the lines between nodes.
Whether to plot points and/or tangent vectors (logical, default: tangent vectors only)
Whether to plot points and/or tangent vectors (logical, default: tangent vectors only)
Whether to scale tangent vector length by the value of
alpha
the y/x
aspect ratio, see plot.window
.
Whether the plot should be superimposed on one already present
(default: FALSE
).
whether axes should be drawn.
length of tick mark as fraction of plotting region (negative number is outside graph, positive number is inside, 0 suppresses ticks, 1 creates gridlines).
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)
limits for the horizontal axis (see also boundingbox)
limits for the vertical axis (see also boundingbox)
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
whether to plot lines for all segments in neuron.
whether points should only be drawn for nodes (branch/end points)
whether points should be drawn for all points in neuron.
whether to label plotted points with their id.
Whether to plot all sub trees when the neuron is not fully connected.
the axes for the plot.
the title for the plot
sub title for the plot
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.
the value of alpha to use in plotting the nodes.
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)