point_sets_from_locs {LOMAR} | R Documentation |
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)