I have generated a rather complicated plot and need guidance on it's aesthetics. The plot I've generated is "Plot #1" below. I would like to add the grey concentric background circles (not sure how else to word this) as seen in "Plot #2".
Here is my data for plot #1:
dput(invitro)
structure(list(sample = c("in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro",
"in_vitro", "in_vitro", "in_vitro", "in_vitro", "in_vitro"),
process = c("Cell_cycle", "Cell_cycle", "Cell_cycle", "Cell_cycle",
"Cell_cycle", "ECM", "ECM", "ECM", "ECM", "ECM", "ECM", "ECM",
"ECM", "ECM", "ECM", "ECM", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Immune", "Immune", "Immune",
"Immune", "Immune", "Immune", "Localization", "Localization",
"Localization", "Localization", "Localization", "Localization",
"Localization", "Localization", "Localization", "Localization",
"Localization", "Metabolism", "Metabolism", "Metabolism",
"Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism",
"Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism",
"Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism",
"Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism",
"Metabolism", "Metabolism", "Metabolism", "Metabolism", "Signaling",
"Signaling", "Signaling", "Signaling", "Signaling", "Signaling",
"Signaling", "Signaling", "Signaling", "Signaling", "Signaling",
"Signaling", "Signaling", "Signaling", "Signaling", "Signaling",
"Signaling", "Signaling", "Transcription", "Translation"),
pathway = c("REACTOME_AMPLIFICATION_OF_SIGNAL_FROM_THE_KINETOCHORES",
"REACTOME_CELLULAR_SENESCENCE", "REACTOME_MITOTIC_PROMETAPHASE",
"REACTOME_MITOTIC_SPINDLE_CHECKPOINT", "REACTOME_RESOLUTION_OF_SISTER_CHROMATID_COHESION",
"HALLMARK_ADIPOGENESIS", "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION",
"HALLMARK_MYOGENESIS", "KEGG_ECM_RECEPTOR_INTERACTION", "KEGG_FOCAL_ADHESION",
"REACTOME_ACTIVATION_OF_MATRIX_METALLOPROTEINASES", "REACTOME_COLLAGEN_DEGRADATION",
"REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX", "REACTOME_ELASTIC_FIBRE_FORMATION",
"REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION", "REACTOME_MOLECULES_ASSOCIATED_WITH_ELASTIC_FIBRES",
"HALLMARK_ALLOGRAFT_REJECTION", "HALLMARK_COMPLEMENT", "HALLMARK_HYPOXIA",
"HALLMARK_IL6_JAK_STAT3_SIGNALING", "HALLMARK_INFLAMMATORY_RESPONSE",
"HALLMARK_INTERFERON_ALPHA_RESPONSE", "HALLMARK_INTERFERON_GAMMA_RESPONSE",
"HALLMARK_TNFA_SIGNALING_VIA_NFKB", "HALLMARK_XENOBIOTIC_METABOLISM",
"KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY", "KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION",
"KEGG_APOPTOSIS", "KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY",
"KEGG_CHEMOKINE_SIGNALING_PATHWAY", "KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION",
"KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION",
"KEGG_GRAFT_VERSUS_HOST_DISEASE", "KEGG_HUNTINGTONS_DISEASE",
"KEGG_LEISHMANIA_INFECTION", "KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY",
"KEGG_PATHWAYS_IN_CANCER", "KEGG_PRION_DISEASES", "KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY",
"KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY", "REACTOME_ADAPTIVE_IMMUNE_SYSTEM",
"REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM", "REACTOME_CYTOPROTECTION_BY_HMOX1",
"REACTOME_IMMUNE_SYSTEM", "REACTOME_INNATE_IMMUNE_SYSTEM",
"REACTOME_INTERLEUKIN_1_FAMILY_SIGNALING", "REACTOME_INTERLEUKIN_6_FAMILY_SIGNALING",
"REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION", "REACTOME_NEUTROPHIL_DEGRANULATION",
"REACTOME_SIGNALING_BY_INTERLEUKINS", "REACTOME_TNFS_BIND_THEIR_PHYSIOLOGICAL_RECEPTORS",
"REACTOME_TOLL_LIKE_RECEPTOR_9_TLR9_CASCADE", "HALLMARK_PROTEIN_SECRETION",
"KEGG_LYSOSOME", "KEGG_PROTEIN_EXPORT", "REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION",
"REACTOME_ER_TO_GOLGI_ANTEROGRADE_TRANSPORT", "REACTOME_INTRA_GOLGI_AND_RETROGRADE_GOLGI_TO_ER_TRAFFIC",
"REACTOME_MEMBRANE_TRAFFICKING", "REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION",
"REACTOME_RAB_REGULATION_OF_TRAFFICKING", "REACTOME_RETROGRADE_TRANSPORT_AT_THE_TRANS_GOLGI_NETWORK",
"REACTOME_VESICLE_MEDIATED_TRANSPORT", "HALLMARK_BILE_ACID_METABOLISM",
"HALLMARK_CHOLESTEROL_HOMEOSTASIS", "HALLMARK_FATTY_ACID_METABOLISM",
"HALLMARK_GLYCOLYSIS", "HALLMARK_OXIDATIVE_PHOSPHORYLATION",
"HALLMARK_PEROXISOME", "KEGG_OXIDATIVE_PHOSPHORYLATION",
"KEGG_PROPANOATE_METABOLISM", "KEGG_PYRUVATE_METABOLISM",
"KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS", "KEGG_TYPE_I_DIABETES_MELLITUS",
"KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION", "REACTOME_ALPHA_LINOLENIC_OMEGA3_AND_LINOLEIC_OMEGA6_ACID_METABOLISM",
"REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM", "REACTOME_CHOLESTEROL_BIOSYNTHESIS",
"REACTOME_FATTY_ACID_METABOLISM", "REACTOME_METABOLISM",
"REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES", "REACTOME_METABOLISM_OF_LIPIDS",
"REACTOME_METABOLISM_OF_PROTEINS", "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS",
"REACTOME_METABOLISM_OF_WATER_SOLUBLE_VITAMINS_AND_COFACTORS",
"REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION", "REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE",
"REACTOME_RESPIRATORY_ELECTRON_TRANSPORT", "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS",
"REACTOME_THE_CITRIC_ACID_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT",
"REACTOME_GPCR_LIGAND_BINDING", "REACTOME_RAC1_GTPASE_CYCLE",
"REACTOME_RHO_GTPASE_CYCLE", "REACTOME_RHO_GTPASE_EFFECTORS",
"REACTOME_RHO_GTPASES_ACTIVATE_FORMINS", "REACTOME_SIGNALING_BY_GPCR",
"REACTOME_SIGNALING_BY_RHO_GTPASES_MIRO_GTPASES_AND_RHOBTB3",
"HALLMARK_ANDROGEN_RESPONSE", "HALLMARK_MTORC1_SIGNALING",
"KEGG_ERBB_SIGNALING_PATHWAY", "KEGG_MAPK_SIGNALING_PATHWAY",
"KEGG_PPAR_SIGNALING_PATHWAY", "REACTOME_CELLULAR_RESPONSES_TO_STIMULI",
"REACTOME_SIGNALING_BY_EGFR", "REACTOME_SIGNALING_BY_ERBB4",
"REACTOME_SIGNALING_BY_PDGF", "REACTOME_SIGNALING_BY_RECEPTOR_TYROSINE_KINASES",
"REACTOME_SIGNALING_BY_VEGF", "", ""), label = c("invitro_REACTOME_AMPLIFICATION_OF_SIGNAL_FROM_THE_KINETOCHORES(94)",
"invitro_REACTOME_CELLULAR_SENESCENCE(95)", "invitro_REACTOME_MITOTIC_PROMETAPHASE(193)",
"invitro_REACTOME_MITOTIC_SPINDLE_CHECKPOINT(111)", "invitro_REACTOME_RESOLUTION_OF_SISTER_CHROMATID_COHESION(122)",
"invitro_HALLMARK_ADIPOGENESIS(200)", "invitro_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION(194)",
"invitro_HALLMARK_MYOGENESIS(199)", "invitro_KEGG_ECM_RECEPTOR_INTERACTION(83)",
"invitro_KEGG_FOCAL_ADHESION(197)", "invitro_REACTOME_ACTIVATION_OF_MATRIX_METALLOPROTEINASES(34)",
"invitro_REACTOME_COLLAGEN_DEGRADATION(55)", "invitro_REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX(108)",
"invitro_REACTOME_ELASTIC_FIBRE_FORMATION(39)", "invitro_REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION(246)",
"invitro_REACTOME_MOLECULES_ASSOCIATED_WITH_ELASTIC_FIBRES(32)",
"invitro_HALLMARK_ALLOGRAFT_REJECTION(192)", "invitro_HALLMARK_COMPLEMENT(185)",
"invitro_HALLMARK_HYPOXIA(199)", "invitro_HALLMARK_IL6_JAK_STAT3_SIGNALING(85)",
"invitro_HALLMARK_INFLAMMATORY_RESPONSE(197)", "invitro_HALLMARK_INTERFERON_ALPHA_RESPONSE(94)",
"invitro_HALLMARK_INTERFERON_GAMMA_RESPONSE(188)", "invitro_HALLMARK_TNFA_SIGNALING_VIA_NFKB(196)",
"invitro_HALLMARK_XENOBIOTIC_METABOLISM(196)", "invitro_KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY(67)",
"invitro_KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION(69)", "invitro_KEGG_APOPTOSIS(82)",
"invitro_KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY(75)", "invitro_KEGG_CHEMOKINE_SIGNALING_PATHWAY(175)",
"invitro_KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION(240)",
"invitro_KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION(69)",
"invitro_KEGG_GRAFT_VERSUS_HOST_DISEASE(34)", "invitro_KEGG_HUNTINGTONS_DISEASE(173)",
"invitro_KEGG_LEISHMANIA_INFECTION(66)", "invitro_KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY(118)",
"invitro_KEGG_PATHWAYS_IN_CANCER(336)", "invitro_KEGG_PRION_DISEASES(34)",
"invitro_KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY(108)", "invitro_KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY(97)",
"invitro_REACTOME_ADAPTIVE_IMMUNE_SYSTEM(816)", "invitro_REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM(404)",
"invitro_REACTOME_CYTOPROTECTION_BY_HMOX1(53)", "invitro_REACTOME_IMMUNE_SYSTEM(1775)",
"invitro_REACTOME_INNATE_IMMUNE_SYSTEM(1087)", "invitro_REACTOME_INTERLEUKIN_1_FAMILY_SIGNALING(119)",
"invitro_REACTOME_INTERLEUKIN_6_FAMILY_SIGNALING(22)", "invitro_REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION(132)",
"invitro_REACTOME_NEUTROPHIL_DEGRANULATION(549)", "invitro_REACTOME_SIGNALING_BY_INTERLEUKINS(270)",
"invitro_REACTOME_TNFS_BIND_THEIR_PHYSIOLOGICAL_RECEPTORS(26)",
"invitro_REACTOME_TOLL_LIKE_RECEPTOR_9_TLR9_CASCADE(94)",
"invitro_HALLMARK_PROTEIN_SECRETION(94)", "invitro_KEGG_LYSOSOME(119)",
"invitro_KEGG_PROTEIN_EXPORT(23)", "invitro_REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION(266)",
"invitro_REACTOME_ER_TO_GOLGI_ANTEROGRADE_TRANSPORT(148)",
"invitro_REACTOME_INTRA_GOLGI_AND_RETROGRADE_GOLGI_TO_ER_TRAFFIC(187)",
"invitro_REACTOME_MEMBRANE_TRAFFICKING(562)", "invitro_REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION(1310)",
"invitro_REACTOME_RAB_REGULATION_OF_TRAFFICKING(115)", "invitro_REACTOME_RETROGRADE_TRANSPORT_AT_THE_TRANS_GOLGI_NETWORK(45)",
"invitro_REACTOME_VESICLE_MEDIATED_TRANSPORT(709)", "invitro_HALLMARK_BILE_ACID_METABOLISM(111)",
"invitro_HALLMARK_CHOLESTEROL_HOMEOSTASIS(71)", "invitro_HALLMARK_FATTY_ACID_METABOLISM(155)",
"invitro_HALLMARK_GLYCOLYSIS(200)", "invitro_HALLMARK_OXIDATIVE_PHOSPHORYLATION(195)",
"invitro_HALLMARK_PEROXISOME(102)", "invitro_KEGG_OXIDATIVE_PHOSPHORYLATION(128)",
"invitro_KEGG_PROPANOATE_METABOLISM(31)", "invitro_KEGG_PYRUVATE_METABOLISM(39)",
"invitro_KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS(15)", "invitro_KEGG_TYPE_I_DIABETES_MELLITUS(41)",
"invitro_KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION(45)",
"invitro_REACTOME_ALPHA_LINOLENIC_OMEGA3_AND_LINOLEIC_OMEGA6_ACID_METABOLISM(13)",
"invitro_REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM(20)",
"invitro_REACTOME_CHOLESTEROL_BIOSYNTHESIS(28)", "invitro_REACTOME_FATTY_ACID_METABOLISM(165)",
"invitro_REACTOME_METABOLISM(1769)", "invitro_REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES(254)",
"invitro_REACTOME_METABOLISM_OF_LIPIDS(599)", "invitro_REACTOME_METABOLISM_OF_PROTEINS(1657)",
"invitro_REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS(171)",
"invitro_REACTOME_METABOLISM_OF_WATER_SOLUBLE_VITAMINS_AND_COFACTORS(110)",
"invitro_REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION(37)",
"invitro_REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE(48)",
"invitro_REACTOME_RESPIRATORY_ELECTRON_TRANSPORT(97)", "invitro_REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS(120)",
"invitro_REACTOME_THE_CITRIC_ACID_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT(168)",
"invitro_REACTOME_GPCR_LIGAND_BINDING(411)", "invitro_REACTOME_RAC1_GTPASE_CYCLE(172)",
"invitro_REACTOME_RHO_GTPASE_CYCLE(421)", "invitro_REACTOME_RHO_GTPASE_EFFECTORS(245)",
"invitro_REACTOME_RHO_GTPASES_ACTIVATE_FORMINS(135)", "invitro_REACTOME_SIGNALING_BY_GPCR(626)",
"invitro_REACTOME_SIGNALING_BY_RHO_GTPASES_MIRO_GTPASES_AND_RHOBTB3(620)",
"invitro_HALLMARK_ANDROGEN_RESPONSE(96)", "invitro_HALLMARK_MTORC1_SIGNALING(199)",
"invitro_KEGG_ERBB_SIGNALING_PATHWAY(87)", "invitro_KEGG_MAPK_SIGNALING_PATHWAY(264)",
"invitro_KEGG_PPAR_SIGNALING_PATHWAY(68)", "invitro_REACTOME_CELLULAR_RESPONSES_TO_STIMULI(454)",
"invitro_REACTOME_SIGNALING_BY_EGFR(47)", "invitro_REACTOME_SIGNALING_BY_ERBB4(34)",
"invitro_REACTOME_SIGNALING_BY_PDGF(53)", "invitro_REACTOME_SIGNALING_BY_RECEPTOR_TYROSINE_KINASES(401)",
"invitro_REACTOME_SIGNALING_BY_VEGF(100)", "invitro_", "invitro_"
), label2 = c("REACTOME_AMPLIFICATION_OF_SIGNAL_FROM_THE_KINETOCHORES(94)",
"REACTOME_CELLULAR_SENESCENCE(95)", "REACTOME_MITOTIC_PROMETAPHASE(193)",
"REACTOME_MITOTIC_SPINDLE_CHECKPOINT(111)", "REACTOME_RESOLUTION_OF_SISTER_CHROMATID_COHESION(122)",
"HALLMARK_ADIPOGENESIS(200)", "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION(194)",
"HALLMARK_MYOGENESIS(199)", "KEGG_ECM_RECEPTOR_INTERACTION(83)",
"KEGG_FOCAL_ADHESION(197)", "REACTOME_ACTIVATION_OF_MATRIX_METALLOPROTEINASES(34)",
"REACTOME_COLLAGEN_DEGRADATION(55)", "REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX(108)",
"REACTOME_ELASTIC_FIBRE_FORMATION(39)", "REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION(246)",
"REACTOME_MOLECULES_ASSOCIATED_WITH_ELASTIC_FIBRES(32)",
"HALLMARK_ALLOGRAFT_REJECTION(192)", "HALLMARK_COMPLEMENT(185)",
"HALLMARK_HYPOXIA(199)", "HALLMARK_IL6_JAK_STAT3_SIGNALING(85)",
"HALLMARK_INFLAMMATORY_RESPONSE(197)", "HALLMARK_INTERFERON_ALPHA_RESPONSE(94)",
"HALLMARK_INTERFERON_GAMMA_RESPONSE(188)", "HALLMARK_TNFA_SIGNALING_VIA_NFKB(196)",
"HALLMARK_XENOBIOTIC_METABOLISM(196)", "KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY(67)",
"KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION(69)", "KEGG_APOPTOSIS(82)",
"KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY(75)", "KEGG_CHEMOKINE_SIGNALING_PATHWAY(175)",
"KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION(240)", "KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION(69)",
"KEGG_GRAFT_VERSUS_HOST_DISEASE(34)", "KEGG_HUNTINGTONS_DISEASE(173)",
"KEGG_LEISHMANIA_INFECTION(66)", "KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY(118)",
"KEGG_PATHWAYS_IN_CANCER(336)", "KEGG_PRION_DISEASES(34)",
"KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY(108)", "KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY(97)",
"REACTOME_ADAPTIVE_IMMUNE_SYSTEM(816)", "REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM(404)",
"REACTOME_CYTOPROTECTION_BY_HMOX1(53)", "REACTOME_IMMUNE_SYSTEM(1775)",
"REACTOME_INNATE_IMMUNE_SYSTEM(1087)", "REACTOME_INTERLEUKIN_1_FAMILY_SIGNALING(119)",
"REACTOME_INTERLEUKIN_6_FAMILY_SIGNALING(22)", "REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION(132)",
"REACTOME_NEUTROPHIL_DEGRANULATION(549)", "REACTOME_SIGNALING_BY_INTERLEUKINS(270)",
"REACTOME_TNFS_BIND_THEIR_PHYSIOLOGICAL_RECEPTORS(26)", "REACTOME_TOLL_LIKE_RECEPTOR_9_TLR9_CASCADE(94)",
"HALLMARK_PROTEIN_SECRETION(94)", "KEGG_LYSOSOME(119)", "KEGG_PROTEIN_EXPORT(23)",
"REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION(266)", "REACTOME_ER_TO_GOLGI_ANTEROGRADE_TRANSPORT(148)",
"REACTOME_INTRA_GOLGI_AND_RETROGRADE_GOLGI_TO_ER_TRAFFIC(187)",
"REACTOME_MEMBRANE_TRAFFICKING(562)", "REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION(1310)",
"REACTOME_RAB_REGULATION_OF_TRAFFICKING(115)", "REACTOME_RETROGRADE_TRANSPORT_AT_THE_TRANS_GOLGI_NETWORK(45)",
"REACTOME_VESICLE_MEDIATED_TRANSPORT(709)", "HALLMARK_BILE_ACID_METABOLISM(111)",
"HALLMARK_CHOLESTEROL_HOMEOSTASIS(71)", "HALLMARK_FATTY_ACID_METABOLISM(155)",
"HALLMARK_GLYCOLYSIS(200)", "HALLMARK_OXIDATIVE_PHOSPHORYLATION(195)",
"HALLMARK_PEROXISOME(102)", "KEGG_OXIDATIVE_PHOSPHORYLATION(128)",
"KEGG_PROPANOATE_METABOLISM(31)", "KEGG_PYRUVATE_METABOLISM(39)",
"KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS(15)", "KEGG_TYPE_I_DIABETES_MELLITUS(41)",
"KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION(45)", "REACTOME_ALPHA_LINOLENIC_OMEGA3_AND_LINOLEIC_OMEGA6_ACID_METABOLISM(13)",
"REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM(20)", "REACTOME_CHOLESTEROL_BIOSYNTHESIS(28)",
"REACTOME_FATTY_ACID_METABOLISM(165)", "REACTOME_METABOLISM(1769)",
"REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES(254)",
"REACTOME_METABOLISM_OF_LIPIDS(599)", "REACTOME_METABOLISM_OF_PROTEINS(1657)",
"REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS(171)", "REACTOME_METABOLISM_OF_WATER_SOLUBLE_VITAMINS_AND_COFACTORS(110)",
"REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION(37)", "REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE(48)",
"REACTOME_RESPIRATORY_ELECTRON_TRANSPORT(97)", "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS(120)",
"REACTOME_THE_CITRIC_ACID_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT(168)",
"REACTOME_GPCR_LIGAND_BINDING(411)", "REACTOME_RAC1_GTPASE_CYCLE(172)",
"REACTOME_RHO_GTPASE_CYCLE(421)", "REACTOME_RHO_GTPASE_EFFECTORS(245)",
"REACTOME_RHO_GTPASES_ACTIVATE_FORMINS(135)", "REACTOME_SIGNALING_BY_GPCR(626)",
"REACTOME_SIGNALING_BY_RHO_GTPASES_MIRO_GTPASES_AND_RHOBTB3(620)",
"HALLMARK_ANDROGEN_RESPONSE(96)", "HALLMARK_MTORC1_SIGNALING(199)",
"KEGG_ERBB_SIGNALING_PATHWAY(87)", "KEGG_MAPK_SIGNALING_PATHWAY(264)",
"KEGG_PPAR_SIGNALING_PATHWAY(68)", "REACTOME_CELLULAR_RESPONSES_TO_STIMULI(454)",
"REACTOME_SIGNALING_BY_EGFR(47)", "REACTOME_SIGNALING_BY_ERBB4(34)",
"REACTOME_SIGNALING_BY_PDGF(53)", "REACTOME_SIGNALING_BY_RECEPTOR_TYROSINE_KINASES(401)",
"REACTOME_SIGNALING_BY_VEGF(100)", "", ""), total_genes = c(94L,
95L, 193L, 111L, 122L, 200L, 194L, 199L, 83L, 197L, 34L,
55L, 108L, 39L, 246L, 32L, 192L, 185L, 199L, 85L, 197L, 94L,
188L, 196L, 196L, 67L, 69L, 82L, 75L, 175L, 240L, 69L, 34L,
173L, 66L, 118L, 336L, 34L, 108L, 97L, 816L, 404L, 53L, 1775L,
1087L, 119L, 22L, 132L, 549L, 270L, 26L, 94L, 94L, 119L,
23L, 266L, 148L, 187L, 562L, 1310L, 115L, 45L, 709L, 111L,
71L, 155L, 200L, 195L, 102L, 128L, 31L, 39L, 15L, 41L, 45L,
13L, 20L, 28L, 165L, 1769L, 254L, 599L, 1657L, 171L, 110L,
37L, 48L, 97L, 120L, 168L, 411L, 172L, 421L, 245L, 135L,
626L, 620L, 96L, 199L, 87L, 264L, 68L, 454L, 47L, 34L, 53L,
401L, 100L, NA, NA), total_ccgs = c(18L, 27L, 31L, 21L, 20L,
75L, 71L, 49L, 31L, 61L, 7L, 18L, 31L, 15L, 69L, 13L, 44L,
57L, 58L, 24L, 56L, 21L, 46L, 74L, 54L, 23L, 11L, 24L, 23L,
47L, 50L, 12L, 5L, 32L, 19L, 22L, 85L, 10L, 29L, 29L, 152L,
105L, 12L, 347L, 197L, 30L, 6L, 30L, 110L, 65L, 5L, 25L,
27L, 19L, 6L, 64L, 38L, 56L, 145L, 301L, 33L, 16L, 151L,
32L, 33L, 55L, 38L, 44L, 35L, 19L, 17L, 14L, 5L, 5L, 31L,
6L, 15L, 10L, 43L, 379L, 52L, 142L, 363L, 37L, 23L, 13L,
13L, 16L, 24L, 37L, 46L, 56L, 114L, 54L, 27L, 106L, 159L,
29L, 58L, 21L, 72L, 19L, 111L, 10L, 5L, 12L, 101L, 38L, NA,
NA), percent_ccgs = c(19.1, 28.4, 16.1, 18.9, 16.4, 37.5,
36.6, 24.6, 37.3, 31, 20.6, 32.7, 28.7, 38.5, 28, 40.6, 22.9,
30.8, 29.1, 28.2, 28.4, 22.3, 24.5, 37.8, 27.6, 34.3, 15.9,
29.3, 30.7, 26.9, 20.8, 17.4, 14.7, 18.5, 28.8, 18.6, 25.3,
29.4, 26.9, 29.9, 18.6, 26, 22.6, 19.5, 18.1, 25.2, 27.3,
22.7, 20, 24.1, 19.2, 26.6, 28.7, 16, 26.1, 24.1, 25.7, 29.9,
25.8, 23, 28.7, 35.6, 21.3, 28.8, 46.5, 35.5, 19, 22.6, 34.3,
14.8, 54.8, 35.9, 33.3, 12.2, 68.9, 46.2, 75, 35.7, 26.1,
21.4, 20.5, 23.7, 21.9, 21.6, 20.9, 35.1, 27.1, 16.5, 20,
22, 11.2, 32.6, 27.1, 22, 20, 16.9, 25.6, 30.2, 29.1, 24.1,
27.3, 27.9, 24.4, 21.3, 14.7, 22.6, 25.2, 38, NA, NA), kuiper_q = c(0.0012,
0.0125, 0.0122, 2e-04, 8e-04, 1e-04, 0.00467, 0.03294, 0.00733,
0.011, 0.06331, 0.07337, 0.04565, 1e-04, 0.0372, 0.02391,
0.03531, 0.0168, 1e-04, 0.03294, 1e-04, 0.01069, 0.00467,
1e-04, 0.0028, 1e-04, 1e-04, 0.02623, 0.03438, 0.02383, 0.00733,
0.05186, 0.00825, 0.03438, 0.022, 0.02383, 1e-04, 0.03624,
0.05186, 0.09859, 0.01395, 1e-04, 0.09591, 1e-04, 1e-04,
0.02325, 0.0093, 0.09803, 1e-04, 0.0093, 0.05874, 0.08835,
0.07368, 0.00733, 0.07656, 0.0891, 0.06331, 0.0093, 1e-04,
1e-04, 0.1, 0.07971, 1e-04, 0.00373, 0.00467, 1e-04, 0.0246,
0.00187, 0.01493, 0.04278, 0.07656, 0.05186, 0.08631, 0.01414,
1e-04, 0.06331, 0.05735, 0.0093, 0.0093, 1e-04, 0.05735,
1e-04, 1e-04, 1e-04, 0.04882, 0.08835, 0.03906, 1e-04, 0.05231,
1e-04, 0.09591, 0.09838, 0.05735, 0.05231, 0.05735, 0.06331,
1e-04, 0.0021, 0.00467, 0.01956, 0.02907, 0.0088, 0.09803,
0.0093, 0.05874, 0.05231, 1e-04, 0.09803, NA, NA), magnitude = c(0.582559826,
0.334789974, 0.367966232, 0.618601878, 0.520553268, 0.490244052,
0.254695241, 0.247013005, 0.532014538, 0.317731086, 0.747218473,
0.491456148, 0.412941472, 0.681514401, 0.318569137, 0.686983737,
0.341141256, 0.331189542, 0.415767315, 0.480875865, 0.408730258,
0.531410704, 0.367509243, 0.537304851, 0.385778329, 0.59611243,
0.871394324, 0.45691131, 0.519720738, 0.344841686, 0.430433443,
0.638540767, 0.978329254, 0.298064842, 0.599886507, 0.495453093,
0.296357025, 0.670553195, 0.405714157, 0.409916955, 0.216832681,
0.244216972, 0.648847337, 0.259249587, 0.278109047, 0.495505892,
0.972822689, 0.415253813, 0.300387159, 0.328998705, 0.914947064,
0.325094367, 0.354624042, 0.561322152, 0.83609874, 0.230535549,
0.347326316, 0.358065863, 0.25431701, 0.139571717, 0.356851629,
0.571608025, 0.271620625, 0.412101733, 0.447006888, 0.442015479,
0.342545745, 0.430512551, 0.360361975, 0.445883581, 0.395867754,
0.486159648, 0.843262585, 0.945952319, 0.524976401, 0.825590251,
0.670002655, 0.806687163, 0.532405597, 0.242416496, 0.314447154,
0.325856334, 0.119549173, 0.388613666, 0.43843292, 0.698139313,
0.64221684, 0.596767169, 0.369274112, 0.463945949, 0.339565941,
0.242549001, 0.223714136, 0.293919524, 0.36341721, 0.225174651,
0.22619292, 0.46257228, 0.322177574, 0.534783343, 0.280053812,
0.583310077, 0.160858779, 0.829518638, 0.898320485, 0.775622542,
0.273163265, 0.344254479, NA, NA), ct = c(20.64893598, 21.04530289,
20.32510752, 21.14809143, 20.46167879, 0.42211672, 0.187528931,
1.596337828, 1.086895046, 1.624228644, 1.750740331, 2.7660905,
2.351566425, 22.71278515, 0.173514186, 22.18426129, 21.37568466,
22.17886507, 22.00450933, 22.24507811, 22.81343002, 0.13697552,
22.99807766, 22.82498724, 22.429828, 1.134411986, 22.08253765,
0.458915134, 23.61889386, 23.01425318, 21.24825568, 22.56736556,
21.60888408, 0.050728566, 20.71067644, 21.68058168, 0.804402049,
21.10578762, 23.08288759, 21.95656414, 23.13240619, 0.233786059,
2.429340156, 22.65291008, 22.37586514, 2.584447665, 21.8421251,
22.40809451, 22.09294927, 1.165695637, 22.84175606, 1.061546142,
0.412400186, 21.43588798, 0.259905659, 23.91389312, 0.442668635,
23.99883724, 23.68712085, 0.538985528, 20.76952013, 0.774731557,
23.55739152, 23.3241612, 22.93108521, 23.1419317, 0.755163746,
0.186263778, 23.01795165, 22.30867251, 0.340948153, 20.42674307,
21.64363652, 21.01424442, 1, 21.0398765, 1.658784935, 22.61723633,
23.05640579, 23.4921116, 2.038374067, 23.28879953, 0.526657076,
23.26781127, 23.73585712, 23.99257669, 23.90189195, 0.046540734,
23.34666104, 23.61597507, 21.27086113, 22.25364904, 22.71842443,
20.64329105, 21.196098, 20.92718573, 22.02793785, 0.213580293,
22.18137155, 3.241862497, 22.40222178, 22.86329108, 22.75356464,
2.928440661, 3.63320635, 3.120221108, 23.38750213, 22.02966659,
NA, NA)), class = "data.frame", row.names = c(NA, -110L))
Here is my current code:
invitro %>%
mutate(ct = ifelse(ct > 12, ct - 24, ct)) %>%
ggplot(aes(as.numeric(factor(process)), ct, fill = process)) + # Set up the plot aesthetics
geom_vline(xintercept = 1:6, linewidth = 0, color = 'gray92') + # grey vertical lines at each process step
stat_boxplot(geom = 'errorbar', width = 10, aes(color = process)) + # Error bars at the boxplot boundaries
geom_boxplot(width = 10, linewidth = 0, outlier.colour = NA) + # Boxplot without outline and no outliers
stat_boxplot(geom = 'errorbar', width = 10, aes(ymax = after_stat(middle), ymin = after_stat(middle))) + # Error bars at median level
geom_hline(yintercept = c(-12, -8, -4, 0, 4, 8), linetype = 5, alpha = 0.2) + # Horizontal dashed lines and transparency level of the lines
annotate('rect', xmax = -2, xmin = -Inf, ymin = -Inf, ymax = Inf, fill = 'white') + # White background rectangle for centering text
annotate('text', x = -8, y = 0, label = 'in vitro', fontface = 3, size = 10) + # Text annotation
coord_polar(theta = 'y', start = pi) + # Polar coordinate system for a circular plot
theme_void() + # Remove axis labels, ticks, and background
scale_x_continuous(limits = c(-9, 12)) + # X-axis limits
scale_y_continuous(limits = c(-12, 12), breaks = -12:11, labels = ~sprintf('%02d:00', ifelse(.x < 0, .x + 24,.x))) + # Convert 'ct' to 24-hour time format
theme(axis.text.x = element_text(), legend.position = 'top') + # Customize x-axis labels and Place legend at the top
scale_color_manual(values = c('#f67a74', '#ed9a64', '#99cb60', '#59de38', '#33d691', '#33ccd6',
'#a3acf0', '#df90f3', '#f16cd9')) + # Custom color palette for border color
scale_fill_manual(values = c('#f67a74', '#ed9a64', '#99cb60', '#59de38', '#33d691', '#33ccd6',
'#a3acf0', '#df90f3', '#f16cd9')) # Custom color palette for fill color
You can add geom_vline(xintercept = c(-0.75, 1.00, 2.75, 4.25, 6.00, 7.75), linewidth = 3, color = 'gray92') +
below your firt geom_vline