Errors while using Load10X_Spatial

[long212123]

Hello everyone,

I'm new with Seurat. I'm trying to load my my Visium data into Seurat. However, I didn't see any output of a new Seurat object. Instead, I saw a warning message. I also saw warning message when load library of SeuratData, I don't know whether that's the issue. Please find my command and warning message attached below:

library(Seurat)
Attaching SeuratObject
library(SeuratData)
Registered S3 method overwritten by 'cli':
method from
print.boxx spatstat.geom
There were 12 warnings (use warnings() to see them)

warnings()
Warning messages:
1: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
2: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
3: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
4: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
5: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
6: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
7: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
8: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
9: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
10: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
11: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used
12: In if (is.na(desc)) { ... :
the condition has length > 1 and only the first element will be used

library(ggplot2)
library(patchwork)
library(dplyr)
library(Signac)

Load10X_Spatial(

• data.dir = "E:/Postdoc_Projects/Visium SCseq/Visium Results/sample_unknown_WT4/outs",
  

• filename = "filtered_feature_bc_matrix.h5",
  

• assay = "Spatial",
  

• slice = "slice1",
  

• filter.matrix = TRUE,
  

• to.upper = FALSE,
  

• )
  An object of class Seurat
  32285 features across 1619 samples within 1 assay
  Active assay: Spatial (32285 features, 0 variable features)
  Warning message:
  In sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts[]), :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you

Thanks for your patience.
I really appreciate if anyone can help me!