创建Seurat对象时忽略的两个参数竟然有这样的功能？

###
### Create: Jianming Zeng
### Date:  2023-12-31  
### Email: jmzeng1314@163.com
### Blog: http://www.bio-info-trainee.com/
### Forum:  http://www.biotrainee.com/thread-1376-1-1.html
### CAFS/SUSTC/Eli Lilly/University of Macau
### Update Log: 2023-12-31   First version 
### Update Log: 2024-12-09   by juan zhang (492482942@qq.com)
### 

rm(list=ls())
library(dplyr) 
library(future)
library(Seurat)
library(clustree)
library(cowplot)
library(data.table)
library(qs)
library(Matrix)
getwd()

## read data
samples <- list.files("data/", recursive = F, full.names = F, pattern = "txt")
samples

scRNA_list <- lapply(samples, function(pro){
#pro <- samples[1]
print(pro)
  counts <- fread(file = file.path("data/", pro), data.table = F)
  counts[1:4,1:4]
  rownames(counts) <- counts[, 1]
  counts <- counts[, -1]
  dim(counts)

# 创建Seurat对象
  sce <- CreateSeuratObject(counts = counts, min.cells=3, project = gsub(".txt","", pro) )
return(sce)
})
names(scRNA_list) <- gsub(".txt","", samples)
scRNA_list

## merge
sce.all <- merge(scRNA_list[[1]], y=scRNA_list[-1], add.cell.ids=gsub(".txt","", samples))
sce.all <- JoinLayers(sce.all) # seurat v5
sce.all


# 查看特征
as.data.frame(sce.all@assays$RNA$counts[1:10, 1:2])
head(sce.all@meta.data, 10)
table(sce.all$orig.ident) 

table(sce.all$orig.ident) 

   A1    A2    A3    A4    C1    C2    C3    C4    M1    M2    M3    S1    S4 
 6394  7621  8561  4780  6464  6432  7627 10443  7599  5756  8556 12940 10058

> samples
 [1] "IRI1d_1.txt" "IRI1d_2.txt" "IRI1d_3.txt" "IRI1d_4.txt" "IRI3d_1.txt" "IRI3d_2.txt" "IRI3d_3.txt" "IRI3d_4.txt" "MSC1.txt"    "MSC2.txt"    "MSC3.txt"   
[12] "sham1.txt"   "sham2.txt"

pro <- samples[1]
print(pro)
counts <- fread(file = file.path("data/", pro), data.table = F)
counts[1:4,1:4]
rownames(counts) <- counts[, 1]
counts <- counts[, -1]
dim(counts)

# 创建Seurat对象
sce <- CreateSeuratObject(counts = counts, min.cells=3, project = gsub(".txt","", pro) )
head(sce@meta.data)

> gsub(".txt","", pro)
[1] "IRI1d_1"

Create a Seurat object
Description
Create a Seurat object from raw data

Usage
CreateSeuratObject(
  counts,
  assay = "RNA",
  names.field = 1,
  names.delim = "_",
  meta.data = NULL,
  project = "CreateSeuratObject",
  ...
)

Arguments
counts 
Either a matrix-like object with unnormalized data with cells as columns and features as rows or an Assay-derived object

assay 
Name of the initial assay

names.field 
For the initial identity class for each cell, choose this field from the cell's name. E.g. If your cells are named as BARCODE_CLUSTER_CELLTYPE in the input matrix, set names.field to 3 to set the initial identities to CELLTYPE.

names.delim 
For the initial identity class for each cell, choose this delimiter from the cell's column name. E.g. If your cells are named as BARCODE-CLUSTER-CELLTYPE, set this to “-” to separate the cell name into its component parts for picking the relevant field.

meta.data 
Additional cell-level metadata to add to the Seurat object. Should be a data.frame where the rows are cell names and the columns are additional metadata fields. Row names in the metadata need to match the column names of the counts matrix.

project 
Project name for the Seurat object

# 创建Seurat对象
sce <- CreateSeuratObject(counts = counts, min.cells=3, project = gsub(".txt","", pro), names.field=0 )
head(sce@meta.data)