SMOLR_DBSCAN: Analysis of SMOLR localization data by DBSCAN clustering,...

In ErasmusOIC/SMoLR: Single Molecule Localization Microscopy visualization and analysis in R

Analysis of SMOLR localization data by DBSCAN clustering, using the DBSCAN algorithm from the DBSCAN R package.

Usage

SMOLR_DBSCAN(x, y, ch, prec, eps, MinPts)

Arguments

x	X coordinates in nm, a localizations data.frame or a list of data.frames.
y	Y coordinates in nm
ch	Channel number (default=1)
prec	Precision in nm (default=20)
eps	Size of linking radius. (default = 50)
MinPts	Number of minimum points in the eps region (default =50)

Value

returns a r object of the class smolr_dbscan which is a list containing 4 items.

dbscan	the localization data.frame containing an addition "Cluster" column, indicating the cluster ID as determined by the dbscan algorithm. Cluster=0 is background
parameters	list of parameters of the given data per channel. Nloc number of localizations, max min and mean of x and y coordinates.
clust_parameters	list of parameters of the given data per DBSCAN cluster.
inputs	list of values that were the input in the function, for back reference

The smolrdata object can be used for plotting, see examples.

Author(s)

Optical Imaging Centre ErasmusMC Rotterdam

See Also

dbscan

Examples

x <- SMOLR_DBSCAN(smolrdata)
plot(x)
plot(x,hide_noise = T)

ErasmusOIC/SMoLR documentation built on July 27, 2023, 8:05 p.m.