fcs_to_img {flowCHIC} | R Documentation |
Create histogram images of FCS files.
## S4 method for signature 'character' fcs_to_img(files,transformation=FALSE,ch1="FS.Log",ch2="FL.4.Log",width=300,height=300,...)
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. |
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.
The fcs_to_img() method creates histogram images of FCS files.
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
H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York,2009.
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)