kNearestNeighbour

K nearest neigbour search script combined with Fiji macro

Requirements

• Rscript (added to PATH variable)
• RANN package

To Run

Command Line

Test command

Rscript kNNScript.R test

With input

Rscript kNNScript.R inputA.csv inputB.csv [#k nearest neighbours to find] ouputName plot

Run from Fiji Macro

• NOTE: Absolute paths should be provided to the script or it will read from the Fiji app directory

• a. Specify the absolute path to the working directory

//Specify absolute path to working directory
wd = "C:/Users/...path to working directory.../"

• b. Specify input files, number of nearest neighbours to calculate (k) and output name (should contain no file extension)

Inputs

• Two csv files with X and Y coordinates with no headers

Outputs

• One csv file with the query coordinate set and coordinate sets for k nearest neighbours
• [Optional] Plot with query set and nearest neighbour for each