一、scMetabolism的安裝
scMetabolism是一個R包福铅，用于在單細胞分辨率下量化代謝活性萝毛，目前只適用于物種是人的單細胞數(shù)據(jù)。作者推薦使用seurat的數(shù)據(jù)進行分析滑黔。本文內(nèi)容來自于以下鏈接笆包。
GitHub - wu-yc/scMetabolism：以單細胞分辨率量化代謝活性
#官方的安裝步驟
#先安裝依賴包
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
#如果有些包安裝不上倒彰，嘗試使用BiocManager::install進行安裝英遭，比如GSVA包
BiocManager::install("GSVA")
#安裝scMetabolism
devtools::install_github("wu-yc/scMetabolism")
二、使用
#導入seurat結果
load(file = "pbmc_demo.rda")
#加載R包婿斥，和依賴包
library(scMetabolism)
library(ggplot2)
library(rsvd)
#直接使用seurat對象進行計算汛兜，就這么簡單明了
countexp.Seurat<-sc.metabolism.Seurat(obj = countexp.Seurat, method = "AUCell", imputation = F, ncores = 2, metabolism.type = "KEGG")
# 代謝評分數(shù)據(jù)儲存在：
countexp.Seurat@assays$METABOLISM$score
sc.metabolism.Seurat參數(shù)設置：
obj是一個包含 UMI 計數(shù)矩陣的seurat對象巴粪。
method支持VISION，AUCell粥谬，ssgsea肛根，gsva ，VISION 是默認方法漏策。
imputation允許用戶選擇是否在代謝評分之前插補他們的數(shù)據(jù)派哲。
ncores是并行計算的線程數(shù)。
metabolism.type支持KEGG和REACTOME掺喻，其中KEGG包含83種代謝途徑（官網(wǎng)寫的85芭届，但是實際上只有83），REACTOME包含82種代謝途徑感耙。
附上通路名稱：
- 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
可視化
（1）umap/tsne圖
DimPlot.metabolism(obj = countexp.Seurat, pathway = "Glycolysis / Gluconeogenesis", dimention.reduction.type = "umap", dimention.reduction.run = F, size = 1)
pathway ：是要可視化的興趣路徑褂乍。
dimention.reduction.type：支持和 .umap和tsne
dimention.reduction.run允許用戶選擇是否重新運行給定修拉對象的尺寸縮減。
size:是圖中的點大小抑月。
此函數(shù)返回一個 ggplot 對象树叽，用戶可以對其進行 DIY。
image.png
（2）氣泡圖
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對象數(shù)據(jù)中的一個分組變量谦絮。
norm指根據(jù)行或列縮放值题诵。用戶可以選擇“x”、“y”和“na”层皱。
-
同樣性锭，此函數(shù)返回一個 ggplot 對象，用戶可以對其進行 DIY叫胖。
image.png
（3）箱線圖
BoxPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", ncol = 1)
- ncol：輸出圖像分布成一列草冈。
image.png
