mdftracks (version 0.2.2)

write.mdf: Write an MTrackJ Data File (.mdf)

Description

Writes a data.frame with tracking information as an MTrackJ Data File (.mdf) file. Allows flexible column specification, and to avoid errors the column mapping used for writing is reported back to the user. Writing tracking data in 'id time x y z' format, for example, from the celltrackR package, doesn't require additional arguments.

Usage

write.mdf(
  x,
  file = "",
  cluster.column = NA,
  id.column = 1,
  time.column = 2,
  scale.time = 1,
  pos.columns = c(3, 4, 5),
  channel.column = NA,
  point.column = NA,
  default.channel = 1,
  fileEncoding = ""
)

Arguments

x

the data.frame with track information.

file

either a character string naming a file or a connection open for writing. "" indicates output to the console.

cluster.column

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

id.column

index or name of the column that contains the track ID (either the id in the cluster or a unique id).

time.column

index or name of the column that contains elapsed time

scale.time

a value by which to multiply each time point. Useful for changing units, or specifying the time between positions if the time is given in frames.

pos.columns

vector containing indices or names of the columns that contain the spatial coordinates. If this vector has two entries, the data is assumed to be 2D and the z coordinate is set to 1.0.

channel.column

index or name of the column that contains channel information. If there is no channel column default.channel will be used.

point.column

index or name of the column that contains point ID. If there is no point column, points will be numbered automatically (NB points are not necessarily the same as frames).

default.channel

channel to be used if channel.column is not specified.

fileEncoding

character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See base::file().

See Also

MTrackJ Data Format

celltrackR

Other mdftracks functions: read.mdf()

Examples

if (FALSE) {
# Output to file
write.mdf(mdftracks.example.data, '~/example.mdf', id.column = 'uid',
          time.column = 't', pos.columns = letters[24:26])
}

# Output to stdout with cluster column
write.mdf(mdftracks.example.data, cluster.column = 'cl',
          id.column = 'id', time.column = 't', pos.columns = letters[24:26])

# Output to stdout using data in (id, t, x, y, z) format
write.mdf(mdftracks.example.data[, c('uid', 't', letters[24:26])])