Attempt to fix scTour/pytorch bug

bimberlabinternal · Jan 30, 2025 · f31d80a · f31d80a
1 parent e75788a
commit f31d80a
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/Utils.R b/R/Utils.R
@@ -326,7 +326,7 @@ ClrNormalizeByGroup <- function(seuratObj, groupingVar, assayName = 'ADT', targe
   if (!is.null(minCellsPerGroup) && !is.na(minCellsPerGroup)) {
     groupValues <- as.character(seuratObj[[groupingVar, drop = TRUE]])
     if (any(is.na(groupValues))) {
-      missing <- unique(seuratObj$BarcodePrefix[[is.na(seuratObj[[groupingVar]])]])
+      missing <- unique(seuratObj$BarcodePrefix[is.na(seuratObj[[groupingVar, drop = TRUE]])])
       stop(paste0('There were NAs for the column: ', groupingVar, '. BarcodePrefix values were: ', paste0(missing, collapse = ',')))
     }
 

diff --git a/inst/scripts/PredictScTourPseudotime.py b/inst/scripts/PredictScTourPseudotime.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 import torch
-import anndata
+from anndata import AnnData
 
 def PredictPseudotime(GEXfile, model_file, ptime_out_file, embedding_out_file):
     #read count data and variable genes