fcs_to_img: FCS files to images

In flowCHIC: Analyze flow cytometric data using histogram information

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

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)

Example output

Loading required package: flowCore
Loading required package: ggplot2
Warning messages:
1: `panel.margin` is deprecated. Please use `panel.spacing` property instead 
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead 
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead 

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