calculate_overlaps_xor: Calculate overlap and XOR images

In flowCHIC: Analyze flow cytometric data using histogram information

Description

Calculate overlap and XOR images for each combination of every subset histogram image.

Usage

## S4 method for signature 'character'
calculate_overlaps_xor(subsets,verbose=FALSE)

Arguments

subsets	List of the subset image files. All files have to be in one folder. See the manual for more information about creating the list.
verbose	logical (default=FALSE). Change to TRUE to print the calculated values to two new files called "Results_overlaps.txt" and "Results_xor.txt" to the working directory.

Details

After saving a list containing the filenames of the subset histogram images this method calculates the XOR and overlap images/values for each combination of every image, returns the values and is able to write the values to two new files called "Results_overlaps.txt" and "Results_xor.txt" (see example section). See reference Koch et al. 2013 for more information about the calculation.

Value

The calculate_overlaps_xor() method calculates the overlap and XOR images and returns a list with two data frames containing the calculated data.

Author(s)

Joachim Schumann [e-mail], Christin Koch [e-mail], Ingo Fetzer [e-mail], Susann Müller [e-mail]

References

Christin Koch, Ingo Fetzer, Hauke Harms, and Susann Müller. CHIC - An Automated Approach for the Detection of Dynamic Variations in Complex Microbial Communities. Cytometry Part A, 2013.

Examples

require(EBImage)

## Calculate the overlap and XOR images
## Save the returned values as a list

# Get a list of the filenames of the FCS files
files <- list.files(system.file("extdata",package="flowCHIC"),
full=TRUE,pattern="*.fcs")
# Create histogram images and save them
fcs_to_img(files)
# Create subsets
img_sub(files,x_start=200,x_end=3500,y_start=1000,y_end=3000,maxv=160)
# Get a list of the filenames of the PNG files
subsets <- list.files(path=paste(getwd(),"chic_subset",sep="/"),full=TRUE,pattern="*.png")
# Calculate and save values as a list
results<-calculate_overlaps_xor(subsets)

## Calculate the overlap and XOR images
## Two new files called "Results_overlaps.txt" and
## "Results_xor.txt" are written to the working directory

# Get a list of the filenames of the FCS files
files <- list.files(system.file("extdata",package="flowCHIC"),
full=TRUE,pattern="*.fcs")
# Create histogram images and save them
fcs_to_img(files)
# Create subsets
img_sub(files,x_start=200,x_end=3500,y_start=1000,y_end=3000,maxv=160)
# Get a list of the filenames of the PNG files
subsets <- list.files(path=paste(getwd(),"chic_subset",sep="/"),full=TRUE,pattern="*.png")
# Calculate
calculate_overlaps_xor(subsets,verbose=TRUE)

flowCHIC documentation built on Nov. 8, 2020, 6:53 p.m.