plot3d.APResult: Plot exemplar neurons/all cluster members after clustering by...

In natverse/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset

Plot exemplar neurons/all cluster members after clustering by affinity propagation

Description

For each cluster, savefun receives the exemplar, the other neurons for the current cluster, all exemplars and the cluster_id (numeric). selected is a list with 0 or 1 named entries for each neuron. An entry can contain up to 3 fields: * keepcluster (TRUE/FALSE) * keep (character vector of neurons) * reject (character vector of neurons)

Usage

## S3 method for class 'APResult'
plot3d(
  x,
  plot = c("exemplars", "bycluster", "all"),
  suppressPlot = FALSE,
  savefun = NULL,
  clusters = NULL,
  soma = TRUE,
  Verbose = TRUE,
  selected = list(),
  selected_file = NULL,
  yaml = TRUE,
  col = NULL,
  ...
)

Arguments

x	An APResult object from apcluster
plot	Whether to plot exemplars or all members of each cluster
suppressPlot	logical indicating that plots should be suppressed.
savefun	Optional function called after each plot is shown
clusters	Names of subset of clusters to plot
soma	Whether to plot somata (default TRUE)
Verbose	logical indicating that output should be verbose.
selected	A list selecting some of the neurons from each cluster (see Details)
selected_file	an optional path to a yaml file to load a selection from.
yaml	logical indicating that selections should be saved as yaml files, not rda files.
col	Optional argument passed to plot3dfc.
...	options passed to plot3dfc when plot=exemplars

Value

list with names of selected neurons for each cluster

See Also

apcluster

Examples

## Not run: 
myselection=plot3d(apres15kv2ns,'bycluster')
myselection=LoadObjsFromRda('myselectionfile.rda')[[1]]
mynewselection=plot3d(apres15kv2ns,'bycluster',selected=myselection)

## End(Not run)

natverse/flycircuit documentation built on Jan. 26, 2023, 6:46 p.m.