From f31d80a136dfc8a23101e228c6e176050a660ab7 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 30 Jan 2025 13:16:39 -0800 Subject: [PATCH] Attempt to fix scTour/pytorch bug --- R/Utils.R | 2 +- inst/scripts/PredictScTourPseudotime.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/Utils.R b/R/Utils.R index 5d205309..7af8d81a 100644 --- 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 index ee7e44bb..e74aa217 100644 --- 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