colors.in.classes.folder {nucim}

Compute colors in classes distribution for folders

Description

Compute colors in classes distribution for folders

Usage

colors.in.classes.folder(
  path,
  color1,
  color2 = NULL,
  N = 7,
  type = "intensity",
  thresh1 = NULL,
  thresh2 = NULL,
  sd1 = 2,
  sd2 = 2,
  col1 = "green",
  col2 = "red",
  cores = 1,
  verbose = FALSE
)

Arguments

path

Path to root folder

color1

Image of first color

color2

Image of second color

N

Maximum number of classes

type

Type of spot definition, see details

thresh1

Threshold for first color image

thresh2

Threshold for second color image

sd1

For automatic threshold, that is: mean(color1)+sd1*sd(color1)

sd2

For automatic threshold of color2

col1

Name of color 1

col2

Name of color 2

cores

Number of cores used in parallel, cores=1 implies no parallelization

verbose

verbose mode

Value

Results are in folder colorsinclasses