point_sets_from_locs: point_sets_from_locs

In LOMAR: Localization Microscopy Data Analysis

point_sets_from_locs

Description

Extracts list of point sets from a data frame of single molecule localization coordinates. By default, uses point set membership indicated in the site column.

Usage

point_sets_from_locs(
  locs = NULL,
  channels = NULL,
  min.cardinality = NULL,
  max.cardinality = NULL,
  crop.size = NULL,
  keep.locprec = TRUE,
  sample.size = NULL,
  ignore.site = FALSE,
  cluster.points = FALSE,
  eps = NULL,
  minPts = NULL
)

Arguments

locs,	a data frame with columns x[nm], y[nm], z[nm] and optionally site[numbers], locprec[nm] and locprecz[nm], other columns are ignored.
channels	vector of integers indicating which channel(s) of a multicolour experiment to extract point sets from.
min.cardinality	filter out point sets with less than the specified number of points.
max.cardinality	filter out point sets with more than the specified number of points.
crop.size	remove points from a set if they are further away than the specified distance from the center of the set.
keep.locprec	logical (default:TRUE). Whether to keep locprec information for each point.
sample.size	returns this number of randomly selected point sets. Selects the point sets after applying eventual filtering.
ignore.site	logical (default: FALSE), set to TRUE if point set membership is not present or needed.
cluster.points	logical (default: FALSE), whether to cluster the points using DBSCAN (only if ignore.site is also TRUE).
eps	DBSCAN parameter, size of the epsilon neighbourhood
minPts	DBSCAN parameter, number of minimum points in the eps region

Value

a list of matrices with columns x,y,z, optionally locprec and name set to the value of the site column (if applicable).

Examples

data.file <- system.file("test_data", "simulated_NUP107_data.csv", package = "LOMAR",
 mustWork = TRUE)
locs <- locs_from_csv(file = data.file, locprec.filter = 20)
point.sets <- point_sets_from_locs(locs, keep.locprec = TRUE, min.cardinality = 15)

LOMAR documentation built on March 18, 2022, 6:05 p.m.