SPIAT 包中的错误define_celltypes(formatted_image, phenotypes = c(“panCK+”, “CD8+”, : 找不到函数“define_celltypes”)

发布于 2025-01-11 15:56:04 字数 1673 浏览 4 评论 0原文

我使用 SPIAT 包（https://cancer-evolution.github.io/ SPIAT/articles/introduction.html）分析人体组织样本中肿瘤和免疫细胞的空间分布模式。该包确实很有用，但是在该包提供的功能之一中，我收到一条错误消息：“define_celltypes(formatted_image, phenotypes = c("panCK+", "CD8+", 中出现错误：找不到函数“define_celltypes”。

我尝试使用所谓的 Define_celltypes 函数来指定每个表型，该函数可用于添加指示细胞类型的列。默认情况下，该列称为 Cell.Type。表型和 Cell.Type 之间的区别在于表型代表细胞上存在的所有标记，但 Cell.Type 是细胞的身份。

这是代码和带有 txt.file 的 R 文件。 https://drive.google.com/drive/folders/1lX9Sprd3IDxz08AcJnZ7WT4UE96MWZCC?usp=分享

非常需要您的帮助！谢谢。

> phenotypes = c("panCK+", "CD8+", "FoxP3+", "CD163+", "PD_L1+") 
> names = c("Tumour", "TILs", "Tregs", "Macrophages", "PD-L1+ cells")
> #SPIAT define_celltypes can be used to add a column indicating the cell type. 
> #By default the column is called Cell.Type. The difference between Phenotype and Cell.
> #Type is that phenotype represents all the markers present on the cell but Cell.Type is the identity of the cell.
> formatted_image <- define_celltypes(formatted_image, 
+                                     phenotypes = c("panCK+", "CD8+", "FoxP3+", "CD163+", "PD_L1+"), 
+                                     names = c("Tumour", "TILs", "Tregs", "Macrophages", "PD-L1+ cells"), 
+                                     column.name = "Cell.Type")
Error in define_celltypes(formatted_image, phenotypes = c("panCK+", "CD8+",  : 
  could not find function "define_celltypes"```

原文

I use the SPIAT package (https://cancer-evolution.github.io/SPIAT/articles/introduction.html) to analyze the spatial distribution patterns of tumor and immune cells in human tissue samples. THe package is really useful, however in one of the functions the package provides I get an error message: "Error in define_celltypes(formatted_image, phenotypes = c("panCK+", "CD8+", :
could not find function "define_celltypes".

I try to specifying each Phenotype using the so-called define_celltypes function which can be used to add a column indicating the cell type. By default the column is called Cell.Type. The difference between Phenotype and Cell.Type is that phenotype represents all the markers present on the cell but Cell.Type is the identity of the cell.

Here is the code and the R file with the txt.file.
https://drive.google.com/drive/folders/1lX9Sprd3IDxz08AcJnZ7WT4UE96MWZCC?usp=sharing

Your help would be much needed! Thank you.

> phenotypes = c("panCK+", "CD8+", "FoxP3+", "CD163+", "PD_L1+") 
> names = c("Tumour", "TILs", "Tregs", "Macrophages", "PD-L1+ cells")
> #SPIAT define_celltypes can be used to add a column indicating the cell type. 
> #By default the column is called Cell.Type. The difference between Phenotype and Cell.
> #Type is that phenotype represents all the markers present on the cell but Cell.Type is the identity of the cell.
> formatted_image <- define_celltypes(formatted_image, 
+                                     phenotypes = c("panCK+", "CD8+", "FoxP3+", "CD163+", "PD_L1+"), 
+                                     names = c("Tumour", "TILs", "Tregs", "Macrophages", "PD-L1+ cells"), 
+                                     column.name = "Cell.Type")
Error in define_celltypes(formatted_image, phenotypes = c("panCK+", "CD8+",  : 
  could not find function "define_celltypes"```

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