fcs_to_img {flowCHIC} | R Documentation

## FCS files to images

### Description

Create histogram images of FCS files.

### Usage

    ## S4 method for signature 'character'
    fcs_to_img(files,transformation=FALSE,ch1="FS.Log",ch2="FL.4.Log",width=300,height=300,...)

### Arguments

`files` | List of all .fcs files. All files have to be in one folder. See the manual for more information about creating the list.
`transformation` | Character string to define the type of data transformation (default=FALSE). Fore more details type "?read.FCS" into R command line.
`ch1` | Character string indicating the first channel of the histogram (x-axis) (default="FS.Log"). See the manual for more details.
`ch2` | Character string indicating the second channel of the histogram (y-axis) (default="FL.4.Log"). See the manual for more details.
`width` | Width (pixel) of the resulting histogram image (default=300).
`height` | Height (pixel) of the resulting histogram image (default=300).
`...` | Additional parameters used for reading the FCS files, for creating the PNG images and for creating the plots. Fore more details type "?read.FCS", "?png" or "??ggplot2" into R command line.

### Details

This method creates histogram images of FCS files using the ggplot method of the package "ggplot2" (see reference Wickham 2009). After creating a list containing the names of the FCS files a new folder called "chic_images" is created in the working directory that contains the histogram images. Choose the two channels that are used for plotting on the x/y-axis.

### Value

The fcs_to_img() method creates histogram images of FCS files.

### 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

H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York,2009.

### Examples

    require(flowCore)
    require(ggplot2)

    ## Write the histogram images of the FCS files that are included
    ## to the package in a new subfolder of the working directory
    ## called "chic_images"

    # 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)

[Package flowCHIC version 1.28.0 Index]