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saeyslab / CytoNorm

R library to normalize cytometry data
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script is interrupted #16

Open kaloshi opened 4 years ago

kaloshi commented 4 years ago

Hello everyone,

I try to use CytoNOrm as FlowJo plugin for the first time. At the following step the script is stopped: "## Step 02 of Initial Workflow ## **> ##################################

fsom <- CytoNorm::prepareFlowSOM(train_data$Path,

  • channels,
  • nCells = 6000,
  • FlowSOM.params = list(xdim = 5,
  • ydim = 5,
  • nClus = nCluster,
  • scale = FALSE),
  • transformList = transformList,
  • seed = 1)

cVals = sort(c(5,nCluster,10,15))

cvs <- testCVs(fsom,

  • cluster_values = cVals)

p <- PlotOverviewCV(fsom, cvs) Error in (function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf", : can file 'Rplots.pdf' not open Calls up: PlotOverviewCV -> -> grid.newpage -> Execution stopped**"

Got an idea? I have already exchanged some packages (ggplot2, ploty..)

Thanks a lot in advance.

Benjamin

kaloshi commented 4 years ago

working on windows 10, with R 3.6.3

tomashhurst commented 4 years ago

There seem to be a few issues online that relate to these error messages. Either something is wrong with the plot itself (so it can't plot properly) or there is an issue with your PDF program.

In the R console, could you run session_info() and post the results? This will provide R and package versions etc.