img_sub {flowCHIC} | R Documentation

## Create image subsets

### Description

Create subsets of FCS files and the resulting histogram images.

### Usage

    ## S4 method for signature 'character'
    img_sub(files,transformation=FALSE,ch1="FS.Log",ch2="FL.4.Log",x_start=0,x_end=4095,y_start=0,y_end=4095,xbin=128,maxv=200,width=300,height=300,...)

### Arguments

`files` | Character list of .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.
`x_start` | Start of the rectangle gate on the x-axis (default=0). See the manual for more details.
`x_end` | End of the rectangle gate on the x-axis (default=4095). See the manual for more details.
`y_start` | Start of the rectangle gate on the y-axis (default=0). See the manual for more details.
`y_end` | End of the rectangle gate on the y-axis (default=4095). See the manual for more details.
`xbin` | Number of bins within the histogram (default=128).
`maxv` | Maximal value of the expressions within the histogram that is set to the highest color value (black) (default=200). 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, creating the PNG images and for plotting. For more details type "?read.FCS", "?png" or "??ggplot2" into R command line.

### Details

This method creates subsets of FCS files and the resulting histogram images 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_subset" is created in the working directory that contains the subset histogram images. Choose the two channels that are used for plotting on the x/y-axis. Define the start and the end of the rectangle gate of both axes. See the manual for more details.

### Value

The img_sub() method creates subsets of the histogram images.

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

    # Get a list of the filenames of the FCS files
    files <- list.files(system.file("extdata",package="flowCHIC"),
    full=TRUE,pattern="*.fcs")
    # Create subsets
    img_sub(files,x_start=200,x_end=3500,y_start=1000,y_end=3000,maxv=160)

[Package flowCHIC version 1.28.0 Index]