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【scMetabolism】One-stop metabolic pathway gene set scoring

    

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

    

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    devtools::install_github("YosefLab/VISION")

    

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

    

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    load(file = "pbmc_demo.rda")

    

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    library(scMetabolism)

    

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    library(ggplot2)

    

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    library(rsvd)

    

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quantify single cell metabolism in seurat

    

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

    

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     <- @assays$METABOLISM$score
    

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 dimplot

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

dotplot

    

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

    

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

    

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boxplot

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