Given the position of a particle along its trajectory (a tracklet) and a reference matrix indicating the location of areas of interest in the same coordinates system as those specifying the particle' position, this function retrieve the value (area of interest) given by the reference matrix for the corresponding coordinates over the particle' trajectory.
Arguments
- refDat
A matrix or dataframe or path to a file (either .txt or .csv) containing a distance matrix to any object or the location of one or several areas of interest (e.g., create a distance map using ImageJ - with x and y coordinates as columns and rows names respectively).
- df
A data frame containing x and y coordinates in columns named "x.pos", "y.pos" for a given tracklet.
- sep
The field separator character, the values on each line of the file are separated by this character (optional, needed only if refDat argument is a path).
- dec
The character used in the file for decimal points (optional, needed only if refDat is a path).
- Fun
A custom function used to transform the data from df (e.g., round, ceiling, log). NB: Indeed, while the tracking software generally return cartesian coordinates (x and y) as decimal numbers, distances map does not, it could hence be necessary to round the x and y coordinates to find correspondences with refDat.
Value
This function returns a vector containing the position of a particle over its trajectory according to a distance matrix to any object or a matrix containing the location of an area of interest.
See also
locROI, circles, polygon
Examples
if (FALSE) {
# Download the first dataset from the sample data repository
Path2Data <- MoveR::DLsampleData(dataSet = 1, tracker = "TRex")
Path2Data
# Import the list containing the 9 vectors classically used for further computation
# and flip Y coordinates to start on the bottom-left
trackDat <- MoveR::readTrex(Path2Data[[1]],
flipY = T,
imgHeight = 2160,
rawDat = F)
str(trackDat)
# Import the reference dataset (A matrix or dataframe or path to a file (either .txt or .csv) containing a distance matrix to any object or
# the location of one or several areas of interest (here we have created a distance map using ImageJ)
refDat <- as.matrix(read.delim(Path2Data[[2]],
dec = "."))
## retrieve the value of the edge limit (1) and of the center limit (254) to plot them
arenaEdge <-
stats::setNames(data.frame(which(refDat == 1, arr.ind = T)),
c("y.pos", "x.pos"))
arenaCenter <-
stats::setNames(data.frame(which(refDat == 254, arr.ind = T)),
c("y.pos", "x.pos"))
## then specify that all values above 254 are considered as the center and the remaning at the edge
refDat <-
apply(refDat, 2, function(x)
ifelse(x > 254, "center", "edge"))
# retrieve the area where the particles
# are located over their whole trajectory using locPos function
trackDat <- MoveR::analyseTracklets(trackDat,
customFunc = list(
Position = function(x)
locPos(
refDat,
x,
Fun = function(y)
ifelse(round(y, digits = 0) == 0,
ceiling(y),
round(y, digits = 0))
)
))
# draw the result, with tracklets part that are on the edge of the arena colored in red
# and those at the center in black
MoveR::drawTracklets(trackDat,
add2It = list(
points(x = arenaEdge[["x.pos"]], y = arenaEdge[["y.pos"]], cex = 0.01),
points(x = arenaCenter[["x.pos"]], y = arenaCenter[["y.pos"]], cex = 0.01)
),
colId = "Position")
}