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
bottomleft for the origin, whilst most graphics software uses the
topleft. 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 modifying the AxisDirections argument.
Other neuron:
neuron()
,
ngraph()
,
potential_synapses()
,
prune()
,
resample()
,
rootpoints()
,
spine()
,
subset.neuron()
# Clear the current plot and draw the third neuron from a different view plot(Cell07PNs[[3]], PlotAxes="YZ")