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 |
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
|
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). |
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 modfiying 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)