Hey Tom,
I agree, it seems that cytofkit doesn't reveal raw cell counts (rather than percentages) through the GUI or in the pre-calculated .csv files. The good news is, you can do it yourself quite easily in R with one line of code.
Try this:
1. Quit the R GUI or Rstudio, if you it's already running. This is only to make sure we're starting from a clean slate.
2. Double-click the .RData file that cytofkit saved on your hard drive. Usually this action will cause Rstudio to open up and load the data directly. If not, start Rstudio manually, and use File --> Open to load the .Rdata file.
3. Click "Yes" when Rstudio asks about loading the data into the global environment.
4. In the R console, paste in the line of code below, and hit enter. This should write a new CSV file in the working directory:
- Code:
write.csv(x=table(cbind.data.frame(sample_name=gsub(x=names(analysis_results$clusterRes$Rphenograph), pattern="\\_(?:.(?!\\_))+$", replacement="", perl=T), cluster=analysis_results$clusterRes$Rphenograph)), file="Cell counts per PhenoGraph cluster by sample.csv")
(if you're not sure where the file was saved, use the command
getwd() to find your current working directory)
Good luck!
ES