一、scMetabolism的安装

scMetabolism是一个R包，用于在单细胞分辨率下量化代谢活性，目前只适用于物种是人的单细胞数据。作者推荐使用seurat的数据进行分析。本文内容来自于以下链接。
GitHub - wu-yc/scMetabolism：以单细胞分辨率量化代谢活性

#官方的安装步骤
#先安装依赖包
install.packages(c("devtools", "data.table", "wesanderson", "Seurat",  "AUCell", "GSEABase", "GSVA", "ggplot2","rsvd"))
devtools::install_github("YosefLab/VISION@v2.1.0") #Please note that the version would be v2.1.0
#如果有些包安装不上，尝试使用BiocManager::install进行安装，比如GSVA包
BiocManager::install("GSVA")
#安装scMetabolism
devtools::install_github("wu-yc/scMetabolism")

二、使用

#导入seurat结果
load(file = "pbmc_demo.rda")
#加载R包，和依赖包
library(scMetabolism)
library(ggplot2)
library(rsvd)
#直接使用seurat对象进行计算，就这么简单明了
countexp.Seurat<-sc.metabolism.Seurat(obj = countexp.Seurat, method = "AUCell", imputation = F, ncores = 2, metabolism.type = "KEGG")
# 代谢评分数据储存在：
countexp.Seurat@assays$METABOLISM$score

sc.metabolism.Seurat参数设置：

• obj是一个包含 UMI 计数矩阵的seurat对象。

• method支持VISION，AUCell，ssgsea，gsva ，VISION 是默认方法。

• imputation允许用户选择是否在代谢评分之前插补他们的数据。

• ncores是并行计算的线程数。

• metabolism.type支持KEGG和REACTOME，其中KEGG包含83种代谢途径（官网写的85，但是实际上只有83），REACTOME包含82种代谢途径。

附上通路名称：

• KEGG

1 Glycolysis / Gluconeogenesis
2 Citrate cycle (TCA cycle)
3 Pentose phosphate pathway
4 Pentose and glucuronate interconversions
5 Fructose and mannose metabolism
6 Galactose metabolism
7 Ascorbate and aldarate metabolism
8 Starch and sucrose metabolism
9 Amino sugar and nucleotide sugar metabolism
10 Pyruvate metabolism
11 Glyoxylate and dicarboxylate metabolism
12 Propanoate metabolism
13 Butanoate metabolism
14 Inositol phosphate metabolism
15 Oxidative phosphorylation
16 Nitrogen metabolism
17 Sulfur metabolism
18 Fatty acid biosynthesis
19 Fatty acid elongation
20 Fatty acid degradation
21 Synthesis and degradation of ketone bodies
22 Steroid biosynthesis
23 Primary bile acid biosynthesis
24 Steroid hormone biosynthesis
25 Glycerolipid metabolism
26 Glycerophospholipid metabolism
27 Ether lipid metabolism
28 Sphingolipid metabolism
29 Arachidonic acid metabolism
30 Linoleic acid metabolism
31 alpha-Linolenic acid metabolism
32 Biosynthesis of unsaturated fatty acids
33 Purine metabolism
34 Pyrimidine metabolism
35 Alanine, aspartate and glutamate metabolism
36 Glycine, serine and threonine metabolism
37 Cysteine and methionine metabolism
38 Valine, leucine and isoleucine degradation
39 Valine, leucine and isoleucine biosynthesis
40 Lysine degradation
41 Arginine biosynthesis
42 Arginine and proline metabolism
43 Histidine metabolism
44 Tyrosine metabolism
45 Phenylalanine metabolism
46 Tryptophan metabolism
47 Phenylalanine, tyrosine and tryptophan biosynthesis
48 beta-Alanine metabolism
49 Taurine and hypotaurine metabolism
50 Phosphonate and phosphinate metabolism
51 Selenocompound metabolism
52 D-Glutamine and D-glutamate metabolism
53 Glutathione metabolism
54 N-Glycan biosynthesis
55 Mucin type O-glycan biosynthesis
56 Mannose type O-glycan biosynthesis
57 Other types of O-glycan biosynthesis
58 Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate
59 Glycosaminoglycan biosynthesis - heparan sulfate / heparin
60 Glycosaminoglycan biosynthesis - keratan sulfate
61 Glycosaminoglycan degradation
62 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
63 Glycosphingolipid biosynthesis - lacto and neolacto series
64 Glycosphingolipid biosynthesis - globo and isoglobo series
65 Glycosphingolipid biosynthesis - ganglio series
66 Other glycan degradation
67 Thiamine metabolism
68 Riboflavin metabolism
69 Vitamin B6 metabolism
70 Nicotinate and nicotinamide metabolism
71 Pantothenate and CoA biosynthesis
72 Biotin metabolism
73 Lipoic acid metabolism
74 Folate biosynthesis
75 One carbon pool by folate
76 Retinol metabolism
77 Porphyrin and chlorophyll metabolism
78 Ubiquinone and other terpenoid-quinone biosynthesis
79 Terpenoid backbone biosynthesis
80 Neomycin, kanamycin and gentamicin biosynthesis
81 Metabolism of xenobiotics by cytochrome P450
82 Drug metabolism - cytochrome P450
83 Drug metabolism - other enzymes

• REACTOME

1 Inositol phosphate metabolism
2 PI metabolism
3 Phospholipid metabolism
4 Metabolism of nucleotides
5 Sulfur amino acid metabolism
6 Glycosaminoglycan metabolism
7 PKA mediated phosphorylation of key metabolic factors
8 Glucagon signaling in metabolic regulation
9 Integration of energy metabolism
10 Chrebp activates metabolic gene expression
11 Pp2a mediated dephosphorylation of key metabolic factors
12 Keratan sulfate keratin metabolism
13 Heparan sulfate heparin hs gag metabolism
14 Glycosphingolipid metabolism
15 Chondroitin sulfate dermatan sulfate metabolism
16 Metabolism of porphyrins
17 Bile acid and bile salt metabolism
18 Metabolism of steroid hormones
19 Cobalamin CBL vitamin B12 transport and metabolism
20 Metabolism of folate and pterines
21 Biotin transport and metabolism
22 Vitamin D calciferol metabolism
23 Nicotinate metabolism
24 Vitamin B1 thiamin metabolism
25 Vitamin C ascorbate metabolism
26 Vitamin B2 riboflavin metabolism
27 Metabolism of water soluble vitamins and cofactors
28 Metabolism of vitamins and cofactors
29 Vitamin B5 pantothenate metabolism
30 Carnitine metabolism
31 Metabolism of nitric oxide NOS3 activation and regulation
32 Metabolism of angiotensinogen to angiotensins
33 Alpha linolenic OMEGA3 and linoleic OMEGA6 acid metabolism
34 Linoleic acid LA metabolism
35 Metabolism of amine derived hormones
36 Arachidonic acid metabolism
37 Hyaluronan metabolism
38 Abacavir transport and metabolism
39 Abacavir metabolism
40 Metabolism of ingested semet sec mesec into H2SE
41 Selenoamino acid metabolism
42 Peptide hormone metabolism
43 Defects in cobalamin B12 metabolism
44 Defects in vitamin and cofactor metabolism
45 Defects in biotin btn metabolism
46 Metabolism of polyamines
47 Diseases associated with glycosaminoglycan metabolism
48 Glyoxylate metabolism and glycine degradation
49 Peroxisomal lipid metabolism
50 Regulation of lipid metabolism by pparalpha
51 Sialic acid metabolism
52 Class C3 metabotropic glutamate pheromone receptors 
53 Sphingolipid metabolism
54 Metabolism of lipids
55 Metabolic disorders of biological oxidation enzymes
56 TP53 regulates metabolic genes
57 Fructose metabolism
58 Diseases of carbohydrate metabolism
59 Diseases of metabolism
60 Surfactant metabolism
61 Diseases associated with surfactant metabolism
62 Defective csf2rb causes pulmonary surfactant metabolism dysfunction 5 smdp5 
63 Metabolism of fat soluble vitamins
64 Pyruvate metabolism
65 Glucose metabolism
66 Creatine metabolism
67 Metabolism of amino acids and derivatives
68 Metabolism of carbohydrates
69 Pyruvate metabolism and citric acid TCA cycle
70 Ketone body metabolism
71 Metabolism of RNA
72 Metabolism of steroids
73 Phenylalanine and tyrosine metabolism
74 Aspartate and asparagine metabolism
75 Phenylalanine metabolism
76 Glutamate and glutamine metabolism
77 Fatty acid metabolism
78 Metabolism of cofactors
79 Triglyceride metabolism
80 Glycogen metabolism
81 Foxo mediated transcription of oxidative stress metabolic and neuronal genes
82 Regulation of glycolysis by fructose 2 6 bisphosphate metabolism

可视化

（1）umap/tsne图

DimPlot.metabolism(obj = countexp.Seurat, pathway = "Glycolysis / Gluconeogenesis", dimention.reduction.type = "umap", dimention.reduction.run = F, size = 1)

• pathway ：是要可视化的兴趣路径。

• dimention.reduction.type：支持和 .umap和tsne

• dimention.reduction.run允许用户选择是否重新运行给定修拉对象的尺寸缩减。

• size:是图中的点大小。

此函数返回一个 ggplot 对象，用户可以对其进行 DIY。

image.png

（2）气泡图

input.pathway<-c("Glycolysis / Gluconeogenesis", "Oxidative phosphorylation", "Citrate cycle (TCA cycle)")
DotPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", norm = "y")

• phenotype:是seurat对象数据中的一个分组变量。

• norm指根据行或列缩放值。用户可以选择“x”、“y”和“na”。

• 同样，此函数返回一个 ggplot 对象，用户可以对其进行 DIY。

  
  image.png

（3）箱线图

BoxPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", ncol = 1)

• ncol：输出图像分布成一列。

image.png

在没有seurat数据的情况下作者是不推荐的，所有这里也不进行记录