spotMsd: Computes minimum spanning distance of xy spot data.

In royfrancis/drtracker: Track zebrafish larvae in assay plates

Description

Computes minimum spanning distance of xy spot data.

Usage

spotMsd(files = NA, wells = 24, filenamediscard = "-Tracks.txt",
  mm = 5.4, exportdata = TRUE, exportplot = TRUE, quiet = FALSE)

Arguments

files	A character or vector of paths or filenames. See details.
wells	A numeric indicating plate format. Either 24 or 48.
filenamediscard	A character for part of the filename to be removed. '-Tracks.txt' is removed by default.
mm	A numeric indicating number of pixels in 1 mm.
exportdata	A logical indicating if data table must be exported as a text file to the working directory.
exportplot	A logical if results must be plotted as a figure and exported to working directory.
quiet	A logical indicating if messages should be printed to console during the run. If FALSE, all output to console is killed except progress bar.

Details

Note that the 'xx-EdgeMarks.txt' file must be present in the working directory for the plot exports to work.
files
A character or vector of paths to files. On windows, use choose.files() for interactive selection. The input files must be tab-delimited decimal as dot (.) text files. The file must contain a minimum of 3 columns named x, y and well. x is a numeric indicating x coordinate and y is a numeric indicating y coordinate of each spot. well indicates well assignment for each spot. Any extra columns are not used. Use output from linkFrames().
A text file with edge marks (filename-EdgeMarks.txt) must be present in the working directory for plotting. The edge marks file is exported by function assignWells().

Value

Returns a dataframe with columns: row, plate names, wells, msd in pixels and millimetre. If exportdata=TRUE, the dataframe is export as a text file in the working directory for each input file.

royfrancis/drtracker documentation built on May 27, 2019, 11:45 p.m.