【scMetabolism】一站式代谢通路基因集打分

(c("devtools", "", "wesanderson", "Seurat", "devtools", "AUCell", "GSEABase", "GSVA", "ggplot2","rsvd"))




 



devtools::install_github("YosefLab/VISION")




devtools::install_github("wu-yc/scMetabolism")

load(file = "pbmc_demo.rda")




 



library(scMetabolism)




library(ggplot2)




library(rsvd)

quantify single cell metabolism in seurat

<-(obj = , method = "VISION", imputation = F, ncores = 2,  = "KEGG")




 



 <- @assays$METABOLISM$score

 dimplot

(obj = , pathway = "Glycolysis / Gluconeogenesis",  = "umap",  = F, size = 1)

dotplot

<-c("Glycolysis / Gluconeogenesis", "Oxidative phosphorylation", "Citrate cycle (TCA cycle)")




(obj = , pathway = , phenotype = "ident", norm = "y")

boxplot

(obj = , pathway = , phenotype = "ident", ncol = 1)