Convert toy data to Seurat object
This toy dataset contains 493 cells from mice in a SingleCellExperiment object.
x <- as.Seurat(sce)
x
#> An object of class Seurat
#> 434 features across 493 samples within 1 assay
#> Active assay: originalexp (434 features, 0 variable features)Preprocess
x <- NormalizeData(x, verbose = FALSE)
x <- FindVariableFeatures(x, verbose = FALSE)
x <- ScaleData(x, verbose = FALSE)
x <- RunPCA(x, verbose = FALSE)
x <- RunUMAP(x, dims = 1:10, verbose = FALSE)
x <- FindNeighbors(x, verbose = FALSE)
x <- FindClusters(x, verbose = FALSE)
DimPlot(x, label = TRUE) + NoLegend()
Find differentially expressed genes
deg <- FindAllMarkers(x, verbose = FALSE)
head(deg)
#> p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
#> Cd19 4.647737e-62 2.880037 1.000 0.316 2.017118e-59 0 Cd19
#> Cd79a 1.837977e-60 2.779207 1.000 0.365 7.976821e-58 0 Cd79a
#> Blk 2.114116e-56 2.664290 0.984 0.261 9.175263e-54 0 Blk
#> Cxcr5 6.386240e-56 2.734605 0.969 0.234 2.771628e-53 0 Cxcr5
#> Cd79b 2.547135e-55 2.668777 1.000 0.508 1.105457e-52 0 Cd79b
#> Iglc3 1.186951e-53 2.614278 1.000 0.412 5.151366e-51 0 Iglc3Add entrezgene annotations
db <- org.Mm.eg.db::org.Mm.eg.db
#>
deg <- deg |> mutate(entrezgene = AnnotationDbi::mapIds(db, deg$gene, "ENTREZID", "SYMBOL"))
#> 'select()' returned 1:1 mapping between keys and columnsFunctional enrichment
res <- run_enrichment(deg, type = "KEGG", org = "Mm")
head(res)
#> cluster Pathway N Up Down
#> path:mmu00010...1 0 Glycolysis / Gluconeogenesis 67 0 0
#> path:mmu00020...2 0 Citrate cycle (TCA cycle) 32 0 0
#> path:mmu00030...3 0 Pentose phosphate pathway 33 0 0
#> path:mmu00040...4 0 Pentose and glucuronate interconversions 35 0 0
#> path:mmu00051...5 0 Fructose and mannose metabolism 36 0 0
#> path:mmu00052...6 0 Galactose metabolism 32 0 0
#> P.Up P.Down adj.P.Up adj.P.Down
#> path:mmu00010...1 1 1 1 1
#> path:mmu00020...2 1 1 1 1
#> path:mmu00030...3 1 1 1 1
#> path:mmu00040...4 1 1 1 1
#> path:mmu00051...5 1 1 1 1
#> path:mmu00052...6 1 1 1 1
res |> filter(adj.P.Up < 0.01) |> arrange(desc(Up))
#> cluster
#> path:mmu04660 3
#> path:mmu04060...2 3
#> path:mmu04659...3 3
#> path:mmu04658...4 3
#> path:mmu05152...5 4
#> path:mmu04060...6 7
#> path:mmu05235...7 3
#> path:mmu05133 4
#> path:mmu04650 7
#> path:mmu04514 3
#> path:mmu05162...11 3
#> path:mmu05171...12 4
#> path:mmu04620 4
#> path:mmu05417 4
#> path:mmu04060...15 5
#> path:mmu05171...16 1
#> path:mmu04640...17 3
#> path:mmu05132 4
#> path:mmu05164...19 4
#> path:mmu05167 4
#> path:mmu05323 4
#> path:mmu05152...22 1
#> path:mmu05340...23 3
#> path:mmu04621 4
#> path:mmu05169 4
#> path:mmu05321...26 4
#> path:mmu04658...27 7
#> path:mmu04640...28 0
#> path:mmu04380 4
#> path:mmu04668 4
#> path:mmu05140...31 4
#> path:mmu05162...32 4
#> path:mmu04061...33 7
#> path:mmu05140...34 1
#> path:mmu05164...35 1
#> path:mmu05142...36 3
#> path:mmu05142...37 4
#> path:mmu04662...38 6
#> path:mmu05321...39 7
#> path:mmu04662...40 0
#> path:mmu04061...41 1
#> path:mmu04640...42 2
#> path:mmu05164...43 2
#> path:mmu04640...44 4
#> path:mmu05134 4
#> path:mmu05235...46 4
#> path:mmu04061...47 5
#> path:mmu04659...48 7
#> path:mmu04064 0
#> path:mmu05340...50 0
#> path:mmu04933 2
#> path:mmu05144 4
#> path:mmu04640...53 5
#> path:mmu05340...54 6
#> path:mmu05140...55 2
#> path:mmu05321...56 2
#> Pathway
#> path:mmu04660 T cell receptor signaling pathway
#> path:mmu04060...2 Cytokine-cytokine receptor interaction
#> path:mmu04659...3 Th17 cell differentiation
#> path:mmu04658...4 Th1 and Th2 cell differentiation
#> path:mmu05152...5 Tuberculosis
#> path:mmu04060...6 Cytokine-cytokine receptor interaction
#> path:mmu05235...7 PD-L1 expression and PD-1 checkpoint pathway in cancer
#> path:mmu05133 Pertussis
#> path:mmu04650 Natural killer cell mediated cytotoxicity
#> path:mmu04514 Cell adhesion molecules
#> path:mmu05162...11 Measles
#> path:mmu05171...12 Coronavirus disease - COVID-19
#> path:mmu04620 Toll-like receptor signaling pathway
#> path:mmu05417 Lipid and atherosclerosis
#> path:mmu04060...15 Cytokine-cytokine receptor interaction
#> path:mmu05171...16 Coronavirus disease - COVID-19
#> path:mmu04640...17 Hematopoietic cell lineage
#> path:mmu05132 Salmonella infection
#> path:mmu05164...19 Influenza A
#> path:mmu05167 Kaposi sarcoma-associated herpesvirus infection
#> path:mmu05323 Rheumatoid arthritis
#> path:mmu05152...22 Tuberculosis
#> path:mmu05340...23 Primary immunodeficiency
#> path:mmu04621 NOD-like receptor signaling pathway
#> path:mmu05169 Epstein-Barr virus infection
#> path:mmu05321...26 Inflammatory bowel disease
#> path:mmu04658...27 Th1 and Th2 cell differentiation
#> path:mmu04640...28 Hematopoietic cell lineage
#> path:mmu04380 Osteoclast differentiation
#> path:mmu04668 TNF signaling pathway
#> path:mmu05140...31 Leishmaniasis
#> path:mmu05162...32 Measles
#> path:mmu04061...33 Viral protein interaction with cytokine and cytokine receptor
#> path:mmu05140...34 Leishmaniasis
#> path:mmu05164...35 Influenza A
#> path:mmu05142...36 Chagas disease
#> path:mmu05142...37 Chagas disease
#> path:mmu04662...38 B cell receptor signaling pathway
#> path:mmu05321...39 Inflammatory bowel disease
#> path:mmu04662...40 B cell receptor signaling pathway
#> path:mmu04061...41 Viral protein interaction with cytokine and cytokine receptor
#> path:mmu04640...42 Hematopoietic cell lineage
#> path:mmu05164...43 Influenza A
#> path:mmu04640...44 Hematopoietic cell lineage
#> path:mmu05134 Legionellosis
#> path:mmu05235...46 PD-L1 expression and PD-1 checkpoint pathway in cancer
#> path:mmu04061...47 Viral protein interaction with cytokine and cytokine receptor
#> path:mmu04659...48 Th17 cell differentiation
#> path:mmu04064 NF-kappa B signaling pathway
#> path:mmu05340...50 Primary immunodeficiency
#> path:mmu04933 AGE-RAGE signaling pathway in diabetic complications
#> path:mmu05144 Malaria
#> path:mmu04640...53 Hematopoietic cell lineage
#> path:mmu05340...54 Primary immunodeficiency
#> path:mmu05140...55 Leishmaniasis
#> path:mmu05321...56 Inflammatory bowel disease
#> N Up Down P.Up P.Down adj.P.Up
#> path:mmu04660 103 20 0 1.464452e-22 1.000000e+00 4.520765e-19
#> path:mmu04060...2 292 17 1 2.165935e-10 3.707289e-01 6.686240e-07
#> path:mmu04659...3 105 17 0 8.136886e-18 1.000000e+00 2.511857e-14
#> path:mmu04658...4 88 16 0 1.179996e-17 1.000000e+00 3.642647e-14
#> path:mmu05152...5 180 15 3 3.494362e-13 1.467898e-02 1.078710e-09
#> path:mmu04060...6 292 15 0 6.949345e-12 1.000000e+00 2.145263e-08
#> path:mmu05235...7 88 14 0 1.087426e-14 1.000000e+00 3.356884e-11
#> path:mmu05133 77 14 2 3.302775e-17 2.065298e-02 1.019567e-13
#> path:mmu04650 121 14 0 5.045401e-16 1.000000e+00 1.557515e-12
#> path:mmu04514 174 13 1 1.832721e-09 2.397921e-01 5.657609e-06
#> path:mmu05162...11 146 13 0 2.058379e-10 1.000000e+00 6.354217e-07
#> path:mmu05171...12 247 13 1 4.951672e-09 5.162910e-01 1.528581e-05
#> path:mmu04620 100 12 1 1.346545e-12 2.529308e-01 4.156785e-09
#> path:mmu05417 216 12 1 1.145228e-08 4.695339e-01 3.535320e-05
#> path:mmu04060...15 292 12 3 5.728956e-11 1.794231e-01 1.768529e-07
#> path:mmu05171...16 247 11 0 3.113301e-08 1.000000e+00 9.610760e-05
#> path:mmu04640...17 94 11 1 2.982159e-10 1.370893e-01 9.205926e-07
#> path:mmu05132 253 11 2 6.048073e-07 1.656711e-01 1.867040e-03
#> path:mmu05164...19 173 11 1 1.240946e-08 3.974279e-01 3.830802e-05
#> path:mmu05167 224 11 1 1.779487e-07 4.820001e-01 5.493276e-04
#> path:mmu05323 87 11 0 7.075462e-12 1.000000e+00 2.184195e-08
#> path:mmu05152...22 180 10 2 1.781740e-08 1.411332e-01 5.500232e-05
#> path:mmu05340...23 36 10 0 2.181559e-13 1.000000e+00 6.734471e-10
#> path:mmu04621 213 10 1 1.040297e-06 4.647851e-01 3.211396e-03
#> path:mmu05169 231 10 4 2.174958e-06 4.087630e-03 6.714094e-03
#> path:mmu05321...26 62 10 1 5.580678e-12 1.650679e-01 1.722755e-08
#> path:mmu04658...27 88 10 0 1.480088e-11 1.000000e+00 4.569031e-08
#> path:mmu04640...28 94 9 12 4.325244e-11 2.155219e-12 1.335203e-07
#> path:mmu04380 128 9 1 1.262280e-07 3.119091e-01 3.896659e-04
#> path:mmu04668 113 9 1 4.264682e-08 2.808940e-01 1.316507e-04
#> path:mmu05140...31 70 9 3 5.772190e-10 1.037513e-03 1.781875e-06
#> path:mmu05162...32 146 9 1 3.904844e-07 3.474310e-01 1.205425e-03
#> path:mmu04061...33 95 9 0 9.021364e-10 1.000000e+00 2.784895e-06
#> path:mmu05140...34 70 8 0 1.865654e-09 1.000000e+00 5.759275e-06
#> path:mmu05164...35 173 8 0 2.257595e-06 1.000000e+00 6.969196e-03
#> path:mmu05142...36 103 8 0 2.257151e-06 1.000000e+00 6.967824e-03
#> path:mmu05142...37 103 8 1 3.116680e-07 2.594752e-01 9.621192e-04
#> path:mmu04662...38 81 8 0 8.276765e-11 1.000000e+00 2.555037e-07
#> path:mmu05321...39 62 8 0 6.887262e-10 1.000000e+00 2.126098e-06
#> path:mmu04662...40 81 7 1 1.651664e-08 4.463087e-01 5.098688e-05
#> path:mmu04061...41 95 7 2 4.538343e-07 4.730381e-02 1.400987e-03
#> path:mmu04640...42 94 7 6 1.839218e-08 5.357728e-08 5.677666e-05
#> path:mmu05164...43 173 7 0 1.222807e-06 1.000000e+00 3.774804e-03
#> path:mmu04640...44 94 7 9 2.408198e-06 2.759358e-12 7.434106e-03
#> path:mmu05134 61 7 2 1.214128e-07 1.328728e-02 3.748013e-04
#> path:mmu05235...46 88 7 1 1.539896e-06 2.261929e-01 4.753659e-03
#> path:mmu04061...47 95 7 1 1.981041e-08 3.811117e-01 6.115475e-05
#> path:mmu04659...48 105 7 0 8.997312e-07 1.000000e+00 2.777470e-03
#> path:mmu04064 105 6 5 2.283756e-06 9.408628e-04 7.049955e-03
#> path:mmu05340...50 36 6 4 3.326661e-09 1.238079e-04 1.026940e-05
#> path:mmu04933 101 6 0 8.323226e-07 1.000000e+00 2.569380e-03
#> path:mmu05144 57 6 0 1.737131e-06 1.000000e+00 5.362525e-03
#> path:mmu04640...53 94 6 5 5.434342e-07 9.914375e-05 1.677581e-03
#> path:mmu05340...54 36 6 0 9.480777e-10 1.000000e+00 2.926716e-06
#> path:mmu05140...55 70 5 2 3.051984e-06 1.143386e-02 9.421473e-03
#> path:mmu05321...56 62 5 0 1.662451e-06 1.000000e+00 5.131986e-03
#> adj.P.Down
#> path:mmu04660 1.000000e+00
#> path:mmu04060...2 1.000000e+00
#> path:mmu04659...3 1.000000e+00
#> path:mmu04658...4 1.000000e+00
#> path:mmu05152...5 1.000000e+00
#> path:mmu04060...6 1.000000e+00
#> path:mmu05235...7 1.000000e+00
#> path:mmu05133 1.000000e+00
#> path:mmu04650 1.000000e+00
#> path:mmu04514 1.000000e+00
#> path:mmu05162...11 1.000000e+00
#> path:mmu05171...12 1.000000e+00
#> path:mmu04620 1.000000e+00
#> path:mmu05417 1.000000e+00
#> path:mmu04060...15 1.000000e+00
#> path:mmu05171...16 1.000000e+00
#> path:mmu04640...17 1.000000e+00
#> path:mmu05132 1.000000e+00
#> path:mmu05164...19 1.000000e+00
#> path:mmu05167 1.000000e+00
#> path:mmu05323 1.000000e+00
#> path:mmu05152...22 1.000000e+00
#> path:mmu05340...23 1.000000e+00
#> path:mmu04621 1.000000e+00
#> path:mmu05169 1.000000e+00
#> path:mmu05321...26 1.000000e+00
#> path:mmu04658...27 1.000000e+00
#> path:mmu04640...28 6.653162e-09
#> path:mmu04380 1.000000e+00
#> path:mmu04668 1.000000e+00
#> path:mmu05140...31 1.000000e+00
#> path:mmu05162...32 1.000000e+00
#> path:mmu04061...33 1.000000e+00
#> path:mmu05140...34 1.000000e+00
#> path:mmu05164...35 1.000000e+00
#> path:mmu05142...36 1.000000e+00
#> path:mmu05142...37 1.000000e+00
#> path:mmu04662...38 1.000000e+00
#> path:mmu05321...39 1.000000e+00
#> path:mmu04662...40 1.000000e+00
#> path:mmu04061...41 1.000000e+00
#> path:mmu04640...42 1.653930e-04
#> path:mmu05164...43 1.000000e+00
#> path:mmu04640...44 8.518138e-09
#> path:mmu05134 1.000000e+00
#> path:mmu05235...46 1.000000e+00
#> path:mmu04061...47 1.000000e+00
#> path:mmu04659...48 1.000000e+00
#> path:mmu04064 1.000000e+00
#> path:mmu05340...50 3.821950e-01
#> path:mmu04933 1.000000e+00
#> path:mmu05144 1.000000e+00
#> path:mmu04640...53 3.060568e-01
#> path:mmu05340...54 1.000000e+00
#> path:mmu05140...55 1.000000e+00
#> path:mmu05321...56 1.000000e+00
res |> filter(adj.P.Down < 0.01) |> arrange(desc(Down))
#> cluster
#> path:mmu04060 0
#> path:mmu05152...2 0
#> path:mmu05142 0
#> path:mmu04640...4 0
#> path:mmu05235...5 0
#> path:mmu05169 5
#> path:mmu04061 0
#> path:mmu04659...8 0
#> path:mmu04660 0
#> path:mmu05133 0
#> path:mmu05417...11 0
#> path:mmu04662...12 5
#> path:mmu05132 5
#> path:mmu05161...14 5
#> path:mmu05166 5
#> path:mmu05167...16 5
#> path:mmu05417...17 5
#> path:mmu04658...18 0
#> path:mmu05135 0
#> path:mmu05162 0
#> path:mmu05323 0
#> path:mmu04640...22 4
#> path:mmu04064...23 5
#> path:mmu04380 5
#> path:mmu05164 5
#> path:mmu04650 0
#> path:mmu05134 0
#> path:mmu05140 0
#> path:mmu04640...29 1
#> path:mmu04210 5
#> path:mmu05152...31 5
#> path:mmu05160 5
#> path:mmu05167...33 8
#> path:mmu04662...34 1
#> path:mmu04620 5
#> path:mmu04625 5
#> path:mmu04657 5
#> path:mmu04668 5
#> path:mmu04659...39 8
#> path:mmu05161...40 8
#> path:mmu05144 0
#> path:mmu04640...42 2
#> path:mmu04662...43 4
#> path:mmu05220 5
#> path:mmu05221 5
#> path:mmu05340...46 5
#> path:mmu04064...47 8
#> path:mmu04658...48 8
#> path:mmu05145 8
#> path:mmu05235...50 8
#> path:mmu05321 8
#> path:mmu05340...52 1
#> path:mmu04662...53 2
#> path:mmu05340...54 2
#> path:mmu05340...55 4
#> Pathway
#> path:mmu04060 Cytokine-cytokine receptor interaction
#> path:mmu05152...2 Tuberculosis
#> path:mmu05142 Chagas disease
#> path:mmu04640...4 Hematopoietic cell lineage
#> path:mmu05235...5 PD-L1 expression and PD-1 checkpoint pathway in cancer
#> path:mmu05169 Epstein-Barr virus infection
#> path:mmu04061 Viral protein interaction with cytokine and cytokine receptor
#> path:mmu04659...8 Th17 cell differentiation
#> path:mmu04660 T cell receptor signaling pathway
#> path:mmu05133 Pertussis
#> path:mmu05417...11 Lipid and atherosclerosis
#> path:mmu04662...12 B cell receptor signaling pathway
#> path:mmu05132 Salmonella infection
#> path:mmu05161...14 Hepatitis B
#> path:mmu05166 Human T-cell leukemia virus 1 infection
#> path:mmu05167...16 Kaposi sarcoma-associated herpesvirus infection
#> path:mmu05417...17 Lipid and atherosclerosis
#> path:mmu04658...18 Th1 and Th2 cell differentiation
#> path:mmu05135 Yersinia infection
#> path:mmu05162 Measles
#> path:mmu05323 Rheumatoid arthritis
#> path:mmu04640...22 Hematopoietic cell lineage
#> path:mmu04064...23 NF-kappa B signaling pathway
#> path:mmu04380 Osteoclast differentiation
#> path:mmu05164 Influenza A
#> path:mmu04650 Natural killer cell mediated cytotoxicity
#> path:mmu05134 Legionellosis
#> path:mmu05140 Leishmaniasis
#> path:mmu04640...29 Hematopoietic cell lineage
#> path:mmu04210 Apoptosis
#> path:mmu05152...31 Tuberculosis
#> path:mmu05160 Hepatitis C
#> path:mmu05167...33 Kaposi sarcoma-associated herpesvirus infection
#> path:mmu04662...34 B cell receptor signaling pathway
#> path:mmu04620 Toll-like receptor signaling pathway
#> path:mmu04625 C-type lectin receptor signaling pathway
#> path:mmu04657 IL-17 signaling pathway
#> path:mmu04668 TNF signaling pathway
#> path:mmu04659...39 Th17 cell differentiation
#> path:mmu05161...40 Hepatitis B
#> path:mmu05144 Malaria
#> path:mmu04640...42 Hematopoietic cell lineage
#> path:mmu04662...43 B cell receptor signaling pathway
#> path:mmu05220 Chronic myeloid leukemia
#> path:mmu05221 Acute myeloid leukemia
#> path:mmu05340...46 Primary immunodeficiency
#> path:mmu04064...47 NF-kappa B signaling pathway
#> path:mmu04658...48 Th1 and Th2 cell differentiation
#> path:mmu05145 Toxoplasmosis
#> path:mmu05235...50 PD-L1 expression and PD-1 checkpoint pathway in cancer
#> path:mmu05321 Inflammatory bowel disease
#> path:mmu05340...52 Primary immunodeficiency
#> path:mmu04662...53 B cell receptor signaling pathway
#> path:mmu05340...54 Primary immunodeficiency
#> path:mmu05340...55 Primary immunodeficiency
#> N Up Down P.Up P.Down adj.P.Up
#> path:mmu04060 292 8 17 9.872823e-06 1.462830e-11 3.047741e-02
#> path:mmu05152...2 180 4 15 4.528637e-03 1.635953e-12 1.000000e+00
#> path:mmu05142 103 1 13 3.249728e-01 2.749525e-13 1.000000e+00
#> path:mmu04640...4 94 9 12 4.325244e-11 2.155219e-12 1.335203e-07
#> path:mmu05235...5 88 0 12 1.000000e+00 9.579758e-13 1.000000e+00
#> path:mmu05169 231 0 12 1.000000e+00 8.586273e-10 1.000000e+00
#> path:mmu04061 95 4 11 4.276364e-04 5.758061e-11 1.000000e+00
#> path:mmu04659...8 105 0 11 1.000000e+00 1.737795e-10 1.000000e+00
#> path:mmu04660 103 0 10 1.000000e+00 2.684998e-09 1.000000e+00
#> path:mmu05133 77 1 10 2.542526e-01 1.444745e-10 1.000000e+00
#> path:mmu05417...11 216 5 10 1.211565e-03 2.969335e-06 1.000000e+00
#> path:mmu04662...12 81 1 10 2.383754e-01 4.981979e-12 1.000000e+00
#> path:mmu05132 253 1 10 5.763515e-01 3.534938e-07 1.000000e+00
#> path:mmu05161...14 163 1 10 4.233419e-01 5.443208e-09 1.000000e+00
#> path:mmu05166 250 2 10 2.029465e-01 3.164720e-07 1.000000e+00
#> path:mmu05167...16 224 3 10 3.791563e-02 1.134665e-07 1.000000e+00
#> path:mmu05417...17 216 3 10 3.458887e-02 8.056182e-08 1.000000e+00
#> path:mmu04658...18 88 1 9 2.850092e-01 1.123087e-08 1.000000e+00
#> path:mmu05135 134 0 9 1.000000e+00 4.420100e-07 1.000000e+00
#> path:mmu05162 146 2 9 1.051687e-01 9.144145e-07 1.000000e+00
#> path:mmu05323 87 0 9 1.000000e+00 1.013942e-08 1.000000e+00
#> path:mmu04640...22 94 7 9 2.408198e-06 2.759358e-12 7.434106e-03
#> path:mmu04064...23 105 4 9 3.829370e-04 1.805059e-09 1.000000e+00
#> path:mmu04380 128 4 9 8.102276e-04 1.053011e-08 1.000000e+00
#> path:mmu05164 173 1 9 4.426769e-01 1.450973e-07 1.000000e+00
#> path:mmu04650 121 0 8 1.000000e+00 2.290225e-06 1.000000e+00
#> path:mmu05134 61 1 8 2.072125e-01 1.053695e-08 1.000000e+00
#> path:mmu05140 70 1 8 2.340158e-01 3.209750e-08 1.000000e+00
#> path:mmu04640...29 94 4 8 1.313250e-03 1.194591e-09 1.000000e+00
#> path:mmu04210 136 0 8 1.000000e+00 3.029926e-07 1.000000e+00
#> path:mmu05152...31 180 5 8 2.905097e-04 2.553649e-06 8.968034e-01
#> path:mmu05160 165 0 8 1.000000e+00 1.326343e-06 1.000000e+00
#> path:mmu05167...33 224 0 8 1.000000e+00 1.373752e-06 1.000000e+00
#> path:mmu04662...34 81 3 7 8.123664e-03 1.321146e-08 1.000000e+00
#> path:mmu04620 100 1 7 2.857586e-01 5.518372e-07 1.000000e+00
#> path:mmu04625 112 3 7 6.003268e-03 1.194284e-06 1.000000e+00
#> path:mmu04657 93 5 7 1.242190e-05 3.352179e-07 3.834639e-02
#> path:mmu04668 113 5 7 3.202147e-05 1.268415e-06 9.885029e-02
#> path:mmu04659...39 105 1 7 7.906677e-02 1.014523e-07 1.000000e+00
#> path:mmu05161...40 163 0 7 1.000000e+00 2.034061e-06 1.000000e+00
#> path:mmu05144 57 3 6 1.262390e-03 3.092574e-06 1.000000e+00
#> path:mmu04640...42 94 7 6 1.839218e-08 5.357728e-08 5.677666e-05
#> path:mmu04662...43 81 2 6 9.897330e-02 8.906365e-08 1.000000e+00
#> path:mmu05220 76 0 6 1.000000e+00 1.886838e-06 1.000000e+00
#> path:mmu05221 70 1 6 2.095690e-01 1.157283e-06 1.000000e+00
#> path:mmu05340...46 36 0 6 1.000000e+00 1.952022e-08 1.000000e+00
#> path:mmu04064...47 105 0 6 1.000000e+00 2.283756e-06 1.000000e+00
#> path:mmu04658...48 88 0 6 1.000000e+00 8.049886e-07 1.000000e+00
#> path:mmu05145 110 0 6 1.000000e+00 2.998824e-06 1.000000e+00
#> path:mmu05235...50 88 0 6 1.000000e+00 8.049886e-07 1.000000e+00
#> path:mmu05321 62 0 6 1.000000e+00 9.791887e-08 1.000000e+00
#> path:mmu05340...52 36 0 5 1.000000e+00 1.698866e-07 1.000000e+00
#> path:mmu04662...53 81 1 5 2.383754e-01 9.582990e-07 1.000000e+00
#> path:mmu05340...54 36 1 5 1.137160e-01 1.507879e-08 1.000000e+00
#> path:mmu05340...55 36 2 4 2.317642e-02 3.055617e-06 1.000000e+00
#> adj.P.Down
#> path:mmu04060 4.515756e-08
#> path:mmu05152...2 5.050187e-09
#> path:mmu05142 8.487784e-10
#> path:mmu04640...4 6.653162e-09
#> path:mmu05235...5 2.957271e-09
#> path:mmu05169 2.650582e-06
#> path:mmu04061 1.777514e-07
#> path:mmu04659...8 5.364572e-07
#> path:mmu04660 8.288588e-06
#> path:mmu05133 4.459927e-07
#> path:mmu05417...11 9.166336e-03
#> path:mmu04662...12 1.537937e-08
#> path:mmu05132 1.091235e-03
#> path:mmu05161...14 1.680318e-05
#> path:mmu05166 9.769491e-04
#> path:mmu05167...16 3.502709e-04
#> path:mmu05417...17 2.486943e-04
#> path:mmu04658...18 3.466970e-05
#> path:mmu05135 1.364485e-03
#> path:mmu05162 2.822798e-03
#> path:mmu05323 3.130038e-05
#> path:mmu04640...22 8.518138e-09
#> path:mmu04064...23 5.572217e-06
#> path:mmu04380 3.250645e-05
#> path:mmu05164 4.479154e-04
#> path:mmu04650 7.069925e-03
#> path:mmu05134 3.252756e-05
#> path:mmu05140 9.908497e-05
#> path:mmu04640...29 3.687704e-06
#> path:mmu04210 9.353383e-04
#> path:mmu05152...31 7.883115e-03
#> path:mmu05160 4.094420e-03
#> path:mmu05167...33 4.240773e-03
#> path:mmu04662...34 4.078377e-05
#> path:mmu04620 1.703522e-03
#> path:mmu04625 3.686755e-03
#> path:mmu04657 1.034818e-03
#> path:mmu04668 3.915598e-03
#> path:mmu04659...39 3.131832e-04
#> path:mmu05161...40 6.279148e-03
#> path:mmu05144 9.546775e-03
#> path:mmu04640...42 1.653930e-04
#> path:mmu04662...43 2.749395e-04
#> path:mmu05220 5.824670e-03
#> path:mmu05221 3.572531e-03
#> path:mmu05340...46 6.025893e-05
#> path:mmu04064...47 7.049955e-03
#> path:mmu04658...48 2.485000e-03
#> path:mmu05145 9.257371e-03
#> path:mmu05235...50 2.485000e-03
#> path:mmu05321 3.022756e-04
#> path:mmu05340...52 5.244398e-04
#> path:mmu04662...53 2.958269e-03
#> path:mmu05340...54 4.654822e-05
#> path:mmu05340...55 9.432690e-03
plot_enrichment(res, padding = grid::unit(c(.5, .5, .5, 6), "cm"), circle.scale = .15)