Error running runSCENIC_3_scoreCells function

[s849]

Hi SCENIC team,

Thank you for developing SCENIC. I have encountered an error when running runSCENIC_3_scoreCells(scenicOptions, logMat). Specifically, the error is associated with the .openDev function. It says it cannot find it. How can I fix this error?

[wulc21]

I also meet the problem, I try the vignette("runSCENIC_3_scoreCells") from http://127.0.0.1:12249/library/SCENIC/doc/detailedStep_3_scoreCells.html#create-rankings, and found the Create rankings step, However I can't solve the problem. Have you solved the problem?

###################### tryCatch({ .openDev(fileName=getIntName(scenicOptions, "aucell_genesStatsPlot"), devType=getSettings(scenicOptions, "devType")) aucellRankings <- AUCell_buildRankings(exprMat, nCores=nCores, plotStats=TRUE, verbose=getSettings(scenicOptions, "verbose")) abline(v=aucellRankings@nGenesDetected["1%"], col="skyblue3", lwd=5, lty=3) dev.off() },error = function(e) { message("Catched error in AUCell_buildRankings() or in the histogram plot: ", e$message) })

[alisyedraza1]

Any solutions?!!

[evy-yiweiwang999]

function .openDev is here https://github.com/aertslab/SCENIC/blob/master/R/priv_openDev.R

.openDev <- function(fileName, devType, ...) { if(devType=="pdf") pdf(paste0(fileName, ".pdf"), ...)

if(devType=="png") png(paste0(fileName, ".png", type="cairo"), ...)

if(devType=="cairo_pfd") # similar to Cairo::CairoPDF? grDevices::cairo_pdf(paste0(fileName, ".pdf"), ...) }