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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error with AUCell_plotTSNE #186

Closed AAA-3 closed 3 years ago

AAA-3 commented 3 years ago

Hello everyone,

I am going through the SCENIC vignette and am trying to creaet and save multiple tSNE plots but am recieving an error with the following code:

aucellApp <- plotTsne_AUCellApp(scenicOptions, exprMat_filtered) # default t-SNE
savedSelections <- shiny::runApp(aucellApp)

#AUCell_plotTSNE() to save static plots:
print(tsneFileName(scenicOptions))
tSNE_scenic <- readRDS(tsneFileName(scenicOptions))
aucell_regulonAUC <- loadInt(scenicOptions, "aucell_regulonAUC")

# Show TF expression:
par(mfrow=c(2,3))
AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Dlx5")],], plots="Expression")
AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Sox10")],], plots="Expression")
AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Sox9")],], plots="Expression")
AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Irf1")],], plots="Expression")
AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Stat6")],], plots="Expression")

The error:

Error in .SummarizedExperiment.charbound(i, rownames(x), fmt) : 
  <aucellResults>[i,] index out of bounds: NA

I have identified the problem lies with the AUCell::AUCell_plotTSNE(tSNE_scenic$Y, exprMat_filtered, aucell_regulonAUC[onlyNonDuplicatedExtended(rownames(aucell_regulonAUC))[c("Irf1")],], plots="Expression") line since all the other plots appear when I try running the line one by one:

image

Anyone have any idea what's going on?

KforKuma commented 3 years ago

met the same problem... I guess this package is almost dead.