2D plots of the elements in a neuronlist, optionally using a subset expression
# S3 method for neuronlist plot( x, subset = NULL, col = NULL, colpal = rainbow, add = NULL, boundingbox = NULL, soma = FALSE, ..., SUBSTITUTE = TRUE )
a neuron list or, for
plot3d.character, a character vector of
neuron names. The default neuronlist used by plot3d.character can be set by
nat for details.
Expression evaluating to logical mask for neurons. See details.
An expression specifying a colour evaluated in the context of the dataframe attached to nl (after any subsetting). See details.
A vector of colours or a function that generates colours
Logical specifying whether to add data to an existing plot or make
a new one. The default value of
NULL creates a new plot with the
first neuron in the neuronlist and then adds the remaining neurons.
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)
Whether to plot a sphere at neuron's origin representing the
soma. Either a logical value or a numeric indicating the radius (default
soma=TRUE the radius is hard coded to 2.
options passed on to plot (such as colours, line width etc)
substitute the expressions passed as
TRUE. For expert
use only, when calling from another function.
list of values of
plot with subsetted dataframe as attribute
The col and subset parameters are evaluated in the context of the dataframe attribute of the neuronlist. If col evaluates to a factor and colpal is a named vector then colours will be assigned by matching factor levels against the named elements of colpal. If there is one unnamed level, this will be used as catch-all default value (see examples).
If col evaluates to a factor and colpal is a function then it will be used to generate colours with the same number of levels as are used in col.
# plot 4 cells plot(Cell07PNs[1:4]) # modify some default plot arguments plot(Cell07PNs[1:4], ylim=c(140,75), main='First 4 neurons') # plot one class of neurons in red and all the others in grey plot(Cell07PNs, col=Glomerulus, colpal=c(DA1='red', 'grey'), WithNodes=FALSE) # subset operation plot(Cell07PNs, subset=Glomerulus%in%c("DA1", "DP1m"), col=Glomerulus, ylim=c(140,75), WithNodes=FALSE)