calculate_overlaps_xor {flowCHIC} | R Documentation

## Calculate overlap and XOR images

### 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 joachim.schumann@ufz.de, Christin Koch christin.koch@ufz.de, Ingo Fetzer info.fetzer@stockholmresilience.su.se, Susann Müller susann.mueller@ufz.de

### 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)

[Package flowCHIC version 1.28.0 Index]