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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: Cannot find cell information named 'CellType (it should be a column of the 'cellInfo') #323

Open SidG13 opened 1 year ago

SidG13 commented 1 year ago

Hi, I'm running into an error with the "plotTsne_compareSettings" function. The error is in the title, and it's the same as in error #121, though that was closed without a solution.

The exact code I ran: plotTsne_compareSettings(fileNames, scenicOptions, showLegend=FALSE, varName = "CellType", cex=.5)

Here's a look at my data:

> fileNames
 [1] "int/tSNE_AUC_05pcs_05perpl.Rds"     "int/tSNE_AUC_05pcs_15perpl.Rds"     "int/tSNE_AUC_05pcs_50perpl.Rds"     "int/tSNE_AUC_15pcs_05perpl.Rds"    
 [5] "int/tSNE_AUC_15pcs_15perpl.Rds"     "int/tSNE_AUC_15pcs_50perpl.Rds"     "int/tSNE_AUC_50pcs_05perpl.Rds"     "int/tSNE_AUC_50pcs_15perpl.Rds"    
 [9] "int/tSNE_AUC_50pcs_30perpl.Rds"     "int/tSNE_AUC_50pcs_50perpl.Rds"     "int/tSNE_oHC_AUC_05pcs_05perpl.Rds" "int/tSNE_oHC_AUC_05pcs_15perpl.Rds"
[13] "int/tSNE_oHC_AUC_05pcs_50perpl.Rds" "int/tSNE_oHC_AUC_15pcs_05perpl.Rds" "int/tSNE_oHC_AUC_15pcs_15perpl.Rds" "int/tSNE_oHC_AUC_15pcs_50perpl.Rds"
[17] "int/tSNE_oHC_AUC_50pcs_05perpl.Rds" "int/tSNE_oHC_AUC_50pcs_15perpl.Rds" "int/tSNE_oHC_AUC_50pcs_50perpl.Rds"
> head(scenicOptions@inputDatasetInfo$cellInfo, n=5)
                   orig.ident nCount_RNA nFeature_RNA percent.mt RNA_snn_res.0.5 CellType
AAACCCAAGACCCGCT-1      tissue       1378          837 1.81422351               0        0
AAACCCATCCGCAGTG-1      tissue       1606          933 1.24533001               0        0
AAACGAAAGTGAATAC-1      tissue       1532         1006 0.06527415               2        2
AAACGAACATCTTCGC-1      tissue       1120          777 0.35714286               0        0
AAAGAACAGACTCATC-1      tissue        277          206 0.00000000               0        0
> type(scenicOptions@inputDatasetInfo$cellInfo$CellType)
[1] "character"

Any ideas? Thanks!