read.tracks.csv {celltrackR}

Read Tracks from Text File

Description

Reads cell tracks from a CSV or other text file. Data are expected to be organized as follows. One column contains a track identifier, which can be numeric or a string, and determines which points belong to the same track. Another column is expected to contain a time index or a time period (e.g. number of seconds elapsed since the beginning of the track, or since the beginning of the experiment). Input of dates is not (yet) supported, as absolute time information is frequently not available. Further columns contain the spatial coordinates. If there are three or less spatial coordinates, their names will by "x", "y", and "z" (depending on whether the tracks are 1D, 2D or 3D). If there are four or more spatial coordinates, their names will be "x1", "x2", and so on. The names or indices of these columns in the CSV files are given using the corresponding parameters (see below). Names and indices can be mixed, e.g. you can specify id.column="Parent" and pos.columns=1:3

Usage

read.tracks.csv(
  file,
  id.column = 1,
  time.column = 2,
  pos.columns = c(3, 4, 5),
  scale.t = 1,
  scale.pos = 1,
  header = TRUE,
  sep = "",
  track.sep.blankline = FALSE,
  ...
)

Arguments

file

the name of the file which the data are to be read from, a readable text-mode connection or a complete URL (see read.table).

id.column

index or name of the column that contains the track ID.

time.column

index or name of the column that contains elapsed time.

pos.columns

vector containing indices or names of the columns that contain the spatial coordinates. If this vector has two entries and the second entry is NA, e.g. c('x',NA) or c(5,NA) then all columns from the indicated column to the last column are used. This is useful when reading files where the exact number of spatial dimensions is not known beforehand.

scale.t

a value by which to multiply each time point. Useful for changing units, or for specifying the time between positions if this is not contained in the file itself.

scale.pos

a value, or a vector of values, by which to multiply each spatial position. Useful for changing units.

header

a logical value indicating whether the file contains the names of the variables as its first line. See read.table.

sep

a character specifying how the colums of the data are separated. The default value "" means columns are separated by tabs or other spaces. See read.table.

track.sep.blankline

logical. If set to TRUE, then tracks are expected to be separated by one or more blank lines in the input file instead of being designated by a track ID column. In this case, numerical track IDs are automatically generated.

...

further arguments to be passed to read.csv, for instance sep="\t" can be useful for tab-separated files.

Details

The input file's first four fields are interpreted as id, pos, t and x, respectively, and, if available, the fifth as y and the sixth as z. The returned object has the class tracks, which is a list of data frames representing the single tracks and having columns t and x, plus y and z, if necessary. The tracks' ids are retained in their position in the list, while the field pos will be unmaintained.

Value

An object of class tracks is returned, which is a list of matrices, each containing the positions of one track. The matrices have a column t, followed by one column for each of the input track's coordinates.