I try to use R with Bioconductor to create a general workflow for the analysis of large flow cytometry datasets. I basically followed this guide.
However, I am stuck with the quality control part. In general the task is to create a folder and write a pdf into it. The code for this is quite easy:
QAdest <- tempdir()
qp1 <- qaProcess.marginevents(flowdata, channels = c("FSC-A","SSC-A"),
outdir = QAdest, pdf = T)
qp2 <- qaProcess.cellnumber(tData, outdir = QAdest, cFactor = 2, pdf = TRUE)
qp3 <- qaProcess.timeline(tData, channels = "FSC-A", outdir = QAdest, cutoff = 1, pdf = TRUE)
qp4 <- qaProcess.timeflow(tData, channels = "FSC-A", outdir = QAdest, cutoff = 2, pdf = TRUE)
url <- writeQAReport(tData, processes = list(qp1, qp2, qp3, qp4), outdir = QAdest, pdf = TRUE)
Unfortunately this code isn't working and I always get the following error message:
Error in system(paste("identify", shQuote(fileName)), intern = TRUE) :
'identify' not found
The variables flowdata and tData were defined as flowsets earlier and work with the other functions. Furthermore, R creates the individual summaries successfully but doesn't define the variables qp1 to qp4 due to the mentioned errors. Therefore the writeQAReport function isn't working.
Also, using another directory (instead of a tempdir folder) isn't working as well. I also reinstalled R and RStudio but it didn't help.
I guess the error is not related to bioconductor itself but to the system call that is made. I couldn't find any solution to this issue and hope you can help me with that.
I am running Windows 10 and use RStudio if that matters.
Thanks a lot!
The line you quote above is trying to invoke a system function identify, which I think is from ImageMagick and so requires ImageMagick to be installed on your computer.
Maybe a more recent workflow (the one you quote is 8 years old) is more helpful?