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, ...)
Arguments
| 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). |
Value
list of plotted points (invisibly)
Details
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.
See also
Other neuron: neuron, ngraph,
potential_synapses, prune,
resample, rootpoints,
spine, subset.neuron
Examples
# Clear the current plot and draw the third neuron from a different view plot(Cell07PNs[[3]], PlotAxes="YZ")
