导入包
library(monocle3)
library(dplyr)
导入10X表达数据
cds <- load_mm_data(mat_path = "./matrix.mtx.gz",
feature_anno_path = "./features.tsv.gz",
cell_anno_path = "./barcodes.tsv.gz")
数据预处理
cds <- preprocess_cds(cds, num_dim = 100)
去批次效应
# cds <- align_cds(cds, alignment_group = "batch") # 报错：Error:
cds <- align_cds(cds)
降维和可视化结果
cds <- reduce_dimension(cds)
alignment_group：subscript contains invalid names
String specifying a column of colData to use for aligning groups of cells. The column specified must be a factor. Alignment can be used to subtract batch effects in a non-linear way. For correcting continuous effects, use residual_model_formula_str. Default is NULL。可以看到需要我们指定一列来作为比对组。
而我通过cellranger获得的表达矩阵等三个数据中，不包含批次信息。因此我才用默认设置。
barcodes.png
features.png
Matrix.png
细胞聚类
# ln -s /opt/conda/pkgs/libgfortran4-7.5.0-h14aa051_20/lib/libgfortran.so.4.0.0 /usr/lib64/libgfortran.so.4
cds = cluster_cells(cds, resolution=1e-5)
注释细胞类型
colData(cds)$assigned_cell_type <- as.character(clusters(cds))
学习轨迹图
cds <- learn_graph(cds)
cds <- order_cells(cds)
