From 5dceeeb333c87e16a309fec6b76b6f8c50309d7f Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 13 Jan 2025 15:31:19 -0600 Subject: [PATCH 1/3] add blueprint name to consensus ref --- .../consensus-cell-type-reference.tsv | 622 +++++++++--------- .../scripts/02-prepare-consensus-reference.R | 7 +- 2 files changed, 317 insertions(+), 312 deletions(-) diff --git a/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv b/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv index da7dcdc61..ee6f169a3 100644 --- a/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv +++ b/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv @@ -1,311 +1,311 @@ -panglao_ontology panglao_annotation original_panglao_name blueprint_ontology blueprint_annotation_main blueprint_annotation_fine consensus_ontology consensus_annotation -CL:0000583 alveolar macrophage Alveolar macrophages CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000767 basophil Basophils CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte -CL:0000771 eosinophil Eosinophils CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte -CL:0000235 macrophage Macrophages CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000097 mast cell Mast cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte Monocytes CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte Osteoclast precursor cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000775 neutrophil Neutrophils CL:0000775 Neutrophils Neutrophils CL:0000775 neutrophil -CL:0000092 osteoclast Osteoclasts CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell Kupffer cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000453 Langerhans cell Langerhans cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000129 microglial cell Microglia CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000767 basophil Basophils CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000451 dendritic cell Dendritic cells CL:0000576 Monocytes Monocytes CL:0000113 mononuclear phagocyte -CL:0000771 eosinophil Eosinophils CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000097 mast cell Mast cells CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000576 monocyte Monocytes CL:0000576 Monocytes Monocytes CL:0000576 monocyte -CL:0000576 monocyte Osteoclast precursor cells CL:0000576 Monocytes Monocytes CL:0000576 monocyte -CL:0000775 neutrophil Neutrophils CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000784 plasmacytoid dendritic cell Plasmacytoid dendritic cells CL:0000576 Monocytes Monocytes CL:0000113 mononuclear phagocyte -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000050 HSC MEP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000050 HSC MEP CL:0008001 hematopoietic precursor cell -CL:0000084 T cell T cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000084 T cell T cells CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000893 thymocyte Thymocytes CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000898 naive T cell T cells naive CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000815 CD4+ T-cells Tregs CL:0000815 regulatory T cell -CL:0000084 T cell T cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000813 memory T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000084 T cell T cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000813 memory T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000084 T cell T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000813 memory T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000084 T cell T cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000813 memory T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000623 natural killer cell NK cells CL:0000623 NK cells NK cells CL:0000623 natural killer cell -CL:0001069 group 2 innate lymphoid cell Nuocytes CL:0000623 NK cells NK cells CL:0001065 innate lymphoid cell -CL:0000236 B cell B cells CL:0000788 B-cells naive B-cells CL:0000236 B cell -CL:0000786 plasma cell Plasma cells CL:0000788 B-cells naive B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell B cells memory CL:0000788 B-cells naive B-cells CL:0000785 mature B cell -CL:0000788 naive B cell B cells naive CL:0000788 B-cells naive B-cells CL:0000788 naive B cell -CL:0000236 B cell B cells CL:0000787 B-cells Memory B-cells CL:0000236 B cell -CL:0000786 plasma cell Plasma cells CL:0000787 B-cells Memory B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell B cells memory CL:0000787 B-cells Memory B-cells CL:0000787 memory B cell -CL:0000788 naive B cell B cells naive CL:0000787 B-cells Memory B-cells CL:0000785 mature B cell -CL:0000236 B cell B cells CL:0000972 B-cells Class-switched memory B-cells CL:0000236 B cell -CL:0000786 plasma cell Plasma cells CL:0000972 B-cells Class-switched memory B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell B cells memory CL:0000972 B-cells Class-switched memory B-cells CL:0000787 memory B cell -CL:0000788 naive B cell B cells naive CL:0000972 B-cells Class-switched memory B-cells CL:0000785 mature B cell -CL:0000646 basal cell Basal cells CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0002322 embryonic stem cell Embryonic stem cells CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000352 epiblast cell Epiblast cells CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000037 HSC HSC CL:0000037 hematopoietic stem cell -CL:0005026 hepatoblast Hepatoblasts CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002248 pluripotent stem cell Pluripotent stem cells CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0002672 retinal progenitor cell Retinal progenitor cells CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002664 cardioblast Cardiac stem and precursor cells CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002250 intestinal crypt stem cell Crypt cells CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000037 HSC HSC CL:0008001 hematopoietic precursor cell -CL:0000324 metanephric mesenchyme stem cell Kidney progenitor cells CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000837 HSC MPP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000837 HSC MPP CL:0008001 hematopoietic precursor cell -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000051 HSC CLP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000051 HSC CLP CL:0008001 hematopoietic precursor cell -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000557 HSC GMP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000557 HSC GMP CL:0008001 hematopoietic precursor cell -CL:0000583 alveolar macrophage Alveolar macrophages CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000767 basophil Basophils CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000771 eosinophil Eosinophils CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000235 macrophage Macrophages CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000097 mast cell Mast cells CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000775 neutrophil Neutrophils CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell Kupffer cells CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000129 microglial cell Microglia CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000084 T cell T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0002038 T follicular helper cell T follicular helper cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte Thymocytes CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0000814 mature NK T cell Natural killer T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell T cells naive CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000912 helper T cell T helper cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000813 memory T cell T memory cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000815 regulatory T cell T regulatory cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000765 erythroblast Erythroblasts CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000558 reticulocyte Reticulocytes CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000556 megakaryocyte Megakaryocytes CL:0000556 HSC Megakaryocytes CL:0000556 megakaryocyte -CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000049 HSC CMP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell Erythroid-like and erythroid precursor cells CL:0000049 HSC CMP CL:0008001 hematopoietic precursor cell -CL:0000583 alveolar macrophage Alveolar macrophages CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000767 basophil Basophils CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000771 eosinophil Eosinophils CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000235 macrophage Macrophages CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000097 mast cell Mast cells CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000775 neutrophil Neutrophils CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell Kupffer cells CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000129 microglial cell Microglia CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000583 alveolar macrophage Alveolar macrophages CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000767 basophil Basophils CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000771 eosinophil Eosinophils CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000235 macrophage Macrophages CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000097 mast cell Mast cells CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000775 neutrophil Neutrophils CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell Kupffer cells CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000129 microglial cell Microglia CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000115 endothelial cell Endothelial cells CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:0002544 aortic endothelial cell Endothelial cells (aorta) CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:2000044 brain microvascular endothelial cell Endothelial cells (blood brain barrier) CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:0000451 dendritic cell Dendritic cells CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000576 monocyte Monocytes CL:0000451 DC DC CL:0000113 mononuclear phagocyte -CL:0000576 monocyte Osteoclast precursor cells CL:0000451 DC DC CL:0000113 mononuclear phagocyte -CL:0000784 plasmacytoid dendritic cell Plasmacytoid dendritic cells CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000453 Langerhans cell Langerhans cells CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000583 alveolar macrophage Alveolar macrophages CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000767 basophil Basophils CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte -CL:0000771 eosinophil Eosinophils CL:0000771 Eosinophils Eosinophils CL:0000771 eosinophil -CL:0000235 macrophage Macrophages CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000097 mast cell Mast cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte Monocytes CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte Osteoclast precursor cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000775 neutrophil Neutrophils CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte -CL:0000092 osteoclast Osteoclasts CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell Kupffer cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000453 Langerhans cell Langerhans cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000129 microglial cell Microglia CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000236 B cell B cells CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000786 plasma cell Plasma cells CL:0000786 B-cells Plasma cells CL:0000786 plasma cell -CL:0000787 memory B cell B cells memory CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000788 naive B cell B cells naive CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000138 chondrocyte Chondrocytes CL:0000138 Chondrocytes Chondrocytes CL:0000138 chondrocyte -CL:2000002 decidual cell Decidual cells CL:0000138 Chondrocytes Chondrocytes CL:0000499 stromal cell -CL:0000632 hepatic stellate cell Hepatic stellate cells CL:0000138 Chondrocytes Chondrocytes CL:0000327 extracellular matrix secreting cell -CL:0000499 stromal cell Stromal cells CL:0000138 Chondrocytes Chondrocytes CL:0000499 stromal cell -CL:0000708 leptomeningeal cell Meningeal cells CL:0000138 Chondrocytes Chondrocytes CL:0000327 extracellular matrix secreting cell -CL:0000057 fibroblast Fibroblasts CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0000632 hepatic stellate cell Hepatic stellate cells CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0002410 pancreatic stellate cell Pancreatic stellate cells CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0002334 preadipocyte Adipocyte progenitor cells CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0000192 smooth muscle cell Smooth muscle cells CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0019019 tracheobronchial smooth muscle cell Airway smooth muscle cells CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0000746 cardiac muscle cell Cardiomyocytes CL:0000192 Smooth muscle Smooth muscle CL:0000187 muscle cell -CL:0000746 cardiac muscle cell Myocytes CL:0000192 Smooth muscle Smooth muscle CL:0000187 muscle cell -CL:0000359 vascular associated smooth muscle cell Pulmonary vascular smooth muscle cells CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0000359 vascular associated smooth muscle cell Vascular smooth muscle cells CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0002068 Purkinje myocyte Purkinje fiber cells CL:0000192 Smooth muscle Smooth muscle CL:0000187 muscle cell -CL:0000622 acinar cell Acinar cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1000488 cholangiocyte Cholangiocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000166 chromaffin cell Chromaffin cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000584 enterocyte Enterocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000164 enteroendocrine cell Enteroendocrine cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000065 ependymal cell Ependymal cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000066 epithelial cell Epithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000160 goblet cell Goblet cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000501 granulosa cell Granulosa cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000182 hepatocyte Hepatocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005006 ionocyte Ionocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000312 keratinocyte Keratinocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000077 mesothelial cell Mesothelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000185 myoepithelial cell Myoepithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000165 neuroendocrine cell Neuroendocrine cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002167 olfactory epithelial cell Olfactory epithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000510 paneth cell Paneth cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000162 parietal cell Parietal cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002481 peritubular myoid cell Peritubular myoid cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000652 pinealocyte Pinealocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000653 podocyte Podocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000209 taste receptor cell Taste receptor cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000731 urothelial cell Urothelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002368 respiratory epithelial cell Airway epithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002370 respiratory goblet cell Airway goblet cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000171 pancreatic A cell Alpha cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000169 type B pancreatic cell Beta cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000706 choroid plexus epithelial cell Choroid plexus cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000158 club cell Clara cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002250 intestinal crypt stem cell Crypt cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000173 pancreatic D cell Delta cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002305 epithelial cell of distal tubule Distal tubule cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002079 pancreatic ductal cell Ductal cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000504 enterochromaffin-like cell Enterochromaffin cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005019 pancreatic epsilon cell Epsilon cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002258 thyroid follicular cell Follicular cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002179 foveolar cell of stomach Foveolar cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000696 PP cell Gamma (PP) cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000155 peptic cell Gastric chief cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002292 type I cell of carotid body Glomus cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005010 renal intercalated cell Intercalated cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1000909 kidney loop of Henle epithelial cell Loop of Henle cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002326 luminal epithelial cell of mammary gland Luminal epithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002327 mammary gland epithelial cell Mammary epithelial cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000242 Merkel cell Merkel cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000682 M cell of gut Microfold cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002199 oxyphil cell of parathyroid gland Oxyphil cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000446 chief cell of parathyroid gland Parathyroid chief cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005009 renal principal cell Principal cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002306 epithelial cell of proximal tubule Proximal tubule cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002062 pulmonary alveolar type 1 cell Pulmonary alveolar type I cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002063 pulmonary alveolar type 2 cell Pulmonary alveolar type II cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1001596 salivary gland glandular cell Salivary mucous cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002140 acinar cell of sebaceous gland Sebocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000216 Sertoli cell Sertoli cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002562 hair germinal matrix cell Trichocytes CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002204 brush cell Tuft cells CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000148 melanocyte Melanocytes CL:0000148 Melanocytes Melanocytes CL:0000148 melanocyte -CL:0000594 skeletal muscle satellite cell Satellite cells CL:0000188 Skeletal muscle Skeletal muscle CL:0000188 cell of skeletal muscle -CL:0000166 chromaffin cell Chromaffin cells CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial 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cell of carotid body Glomus cells CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0000242 Merkel cell Merkel cells CL:0000312 Keratinocytes Keratinocytes CL:0000312 keratinocyte -CL:0002062 pulmonary alveolar type 1 cell Pulmonary alveolar type I cells CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002063 pulmonary alveolar type 2 cell Pulmonary alveolar type II cells CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002140 acinar cell of sebaceous gland Sebocytes CL:0000312 Keratinocytes Keratinocytes CL:0000362 epidermal cell -CL:0000216 Sertoli cell Sertoli cells CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002562 hair germinal matrix cell Trichocytes CL:0000312 Keratinocytes Keratinocytes CL:0000362 epidermal cell -CL:0000115 endothelial cell Endothelial cells CL:2000008 Endothelial cells mv Endothelial cells CL:0000115 endothelial cell -CL:0002544 aortic 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CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000893 thymocyte Thymocytes CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0000084 T cell +CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000898 naive T cell T cells naive CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000912 helper T cell T helper cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000813 memory T cell T memory cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0002419 mature T cell +CL:0000815 regulatory T cell T regulatory cells CL:0000815 CD4+ T-cells Tregs regulatory T cell CL:0000815 regulatory T cell 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CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0000791 mature alpha-beta T cell +CL:0000898 naive T cell T cells naive CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0002419 mature T cell +CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0002419 mature T cell +CL:0000912 helper T cell T helper cells CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0002419 mature T cell +CL:0000813 memory T cell T memory cells CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0000813 memory T cell +CL:0000815 regulatory T cell T regulatory cells CL:0000913 CD8+ T-cells CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0002419 mature T cell +CL:0000623 natural killer cell NK cells CL:0000623 NK cells NK cells natural killer cell CL:0000623 natural killer cell +CL:0001069 group 2 innate lymphoid cell Nuocytes CL:0000623 NK cells NK cells natural killer cell CL:0001065 innate lymphoid cell +CL:0000236 B cell B cells CL:0000788 B-cells naive B-cells naive B cell CL:0000236 B cell +CL:0000786 plasma cell Plasma cells CL:0000788 B-cells naive B-cells naive B cell CL:0000945 lymphocyte of B lineage +CL:0000787 memory B cell B cells memory CL:0000788 B-cells naive B-cells naive B cell CL:0000785 mature B cell +CL:0000788 naive B cell B cells naive CL:0000788 B-cells naive B-cells naive B cell CL:0000788 naive B cell +CL:0000236 B cell B cells CL:0000787 B-cells Memory B-cells memory B cell CL:0000236 B cell +CL:0000786 plasma cell Plasma cells CL:0000787 B-cells Memory B-cells memory B cell CL:0000945 lymphocyte of B lineage +CL:0000787 memory B cell B cells memory CL:0000787 B-cells Memory B-cells memory B cell CL:0000787 memory B cell +CL:0000788 naive B cell B cells naive CL:0000787 B-cells Memory B-cells memory B cell CL:0000785 mature B cell +CL:0000236 B cell B cells CL:0000972 B-cells Class-switched memory B-cells class switched memory B cell CL:0000236 B cell +CL:0000786 plasma cell Plasma cells CL:0000972 B-cells Class-switched memory B-cells class switched memory B cell CL:0000945 lymphocyte of B lineage +CL:0000787 memory B cell B cells memory CL:0000972 B-cells Class-switched memory B-cells class switched memory B cell CL:0000787 memory B cell +CL:0000788 naive B cell B cells naive CL:0000972 B-cells Class-switched memory B-cells class switched memory B cell CL:0000785 mature B cell +CL:0000646 basal cell Basal cells CL:0000037 HSC HSC hematopoietic stem cell CL:0000723 somatic stem cell +CL:0002322 embryonic stem cell Embryonic stem cells CL:0000037 HSC HSC hematopoietic stem cell CL:0000034 stem cell +CL:0000352 epiblast cell Epiblast cells CL:0000037 HSC HSC hematopoietic stem 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cells CL:0000235 Macrophages Macrophages macrophage CL:0000766 myeloid leukocyte +CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000235 Macrophages Macrophages macrophage CL:0000235 macrophage +CL:0000084 T cell T cells CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, alpha-beta T cell CL:0000084 T cell +CL:0002038 T follicular helper cell T follicular helper cells CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, alpha-beta T cell CL:0000791 mature alpha-beta T cell +CL:0000893 thymocyte Thymocytes CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, alpha-beta T cell CL:0000084 T cell +CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, alpha-beta T cell CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, alpha-beta T cell CL:0000791 mature alpha-beta T cell +CL:0000898 naive T cell T cells naive CL:0000625 CD8+ T-cells CD8+ T-cells CD8-positive, 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cells microvascular endothelial cell CL:0000071 blood vessel endothelial cell +CL:2000044 brain microvascular endothelial cell Endothelial cells (blood brain barrier) CL:2000008 Endothelial cells mv Endothelial cells microvascular endothelial cell CL:2000008 microvascular endothelial cell +CL:0000192 smooth muscle cell Smooth muscle cells CL:0000187 Myocytes Myocytes muscle cell CL:0000187 muscle cell +CL:0019019 tracheobronchial smooth muscle cell Airway smooth muscle cells CL:0000187 Myocytes Myocytes muscle cell CL:0000187 muscle cell +CL:0000746 cardiac muscle cell Cardiomyocytes CL:0000187 Myocytes Myocytes muscle cell CL:0000187 muscle cell +CL:0000746 cardiac muscle cell Myocytes CL:0000187 Myocytes Myocytes muscle cell CL:0000187 muscle cell +CL:0000359 vascular associated smooth muscle cell Pulmonary vascular smooth muscle cells CL:0000187 Myocytes Myocytes muscle cell CL:0000187 muscle cell +CL:0000359 vascular associated smooth muscle cell Vascular smooth muscle cells 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+CL:0000706 choroid plexus epithelial cell Choroid plexus cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:4040002 enteroglial cell Enteric glia cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:4042021 neuronal-restricted precursor Immature neurons CL:0000127 Astrocytes Astrocytes astrocyte CL:0000095 neuron associated cell +CL:0000242 Merkel cell Merkel cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000095 neuron associated cell +CL:0000129 microglial cell Microglia CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:0000636 Mueller cell Müller cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:0002453 oligodendrocyte precursor cell Oligodendrocyte progenitor cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000095 neuron associated cell +CL:0002573 Schwann cell Peri-islet Schwann cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:0002573 Schwann cell Schwann cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:0000681 radial glial cell Radial glia cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000125 glial cell +CL:0000516 perineural satellite cell Satellite glial cells CL:0000127 Astrocytes Astrocytes astrocyte CL:0000095 neuron associated cell +CL:0000650 mesangial cell Mesangial cells CL:0000650 Mesangial cells Mesangial cells mesangial cell CL:0000650 mesangial cell +CL:0000669 pericyte Pericytes CL:0000650 Mesangial cells Mesangial cells mesangial cell CL:0000669 pericyte diff --git a/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R b/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R index 3915685a0..8d83ffe8f 100644 --- a/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R +++ b/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R @@ -43,7 +43,11 @@ blueprint_df <- data.frame( blueprint_annotation_fine = blueprint_ref$label.fine ) |> unique() |> - tidyr::drop_na() + tidyr::drop_na() |> + # add in the actual name for the ontology from CL + dplyr::mutate( + blueprint_annotation_cl = cl_ont$name[blueprint_ontology] + ) # Get LCA and descendants ------------------------------------------------------ @@ -121,6 +125,7 @@ consensus_labels_df <- lca_df |> blueprint_ontology, blueprint_annotation_main, blueprint_annotation_fine, + blueprint_annotation_cl, consensus_ontology = lca, consensus_annotation = cl_annotation ) From d0689c34187137c16e5c8108e9e8ccd09f197da8 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 13 Jan 2025 15:31:47 -0600 Subject: [PATCH 2/3] add cl name for blueprint to results --- .../scripts/04-combine-celltype-tables.R | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R b/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R index 453f2d4a9..049224200 100644 --- a/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R +++ b/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R @@ -21,13 +21,13 @@ option_list <- list( ), make_option( opt_str = c("--panglao_ref_file"), - default = file.path(project_root, "references", "panglao-cell-type-ontologies.tsv"), + default = file.path(project_root, "analyses", "cell-type-consensus", "references", "panglao-cell-type-ontologies.tsv"), type = "character", help = "Path to file with panglao assignments and associated cell ontology ids" ), make_option( opt_str = c("--consensus_ref_file"), - default = file.path(project_root, "references", "consensus-cell-type-reference.tsv"), + default = file.path(project_root, "analyses", "cell-type-consensus", "references", "consensus-cell-type-reference.tsv"), type = "character", help = "Path to file containing the reference for assigning consensus cell type labels" ), @@ -73,11 +73,15 @@ consensus_ref_df <- readr::read_tsv(opt$consensus_ref_file) |> # grab singler ref from celldex blueprint_ref <- celldex::BlueprintEncodeData() +# grab obo file, we need this to map the ontologies from blueprint +cl_ont <- ontologyIndex::get_ontology("http://purl.obolibrary.org/obo/cl/releases/2024-09-26/cl-basic.obo") + + # get ontologies and human readable name into data frame for blueprint -# in scpca-nf we don't include the fine label so this lets us add it in +# in scpca-nf we don't include the cl name so this lets us add it in blueprint_df <- data.frame( blueprint_ontology = blueprint_ref$label.ont, - blueprint_annotation_fine = blueprint_ref$label.fine + blueprint_annotation_cl = cl_ont$name[blueprint_ref$label.ont] ) |> unique() |> tidyr::drop_na() From ccbebe20e14d20a0752cb990095358ba1a687934 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 13 Jan 2025 15:33:54 -0600 Subject: [PATCH 3/3] add blueprint_annotation_cl to docs --- analyses/cell-type-consensus/README.md | 2 +- analyses/cell-type-consensus/references/README.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/analyses/cell-type-consensus/README.md b/analyses/cell-type-consensus/README.md index 9789083d4..745327639 100644 --- a/analyses/cell-type-consensus/README.md +++ b/analyses/cell-type-consensus/README.md @@ -81,7 +81,7 @@ The `scpca-consensus-celltype-assignments.tsv` file contains cell type annotatio | `cellassign_celltype_annotation` | Cell type assigned by `CellAssign`; this term is the original term found in the `PanglaoDB` reference file | | `panglao_ontology` | Cell type ontology term associated with the term found in `cellassign_celltype_annotation` column | | `panglao_annotation` | Name associated with the cell type ontology term in `panglao_ontology` | -| `blueprint_annotation_fine` | Fine grained cell type annotation (`label.fine`) from `BlueprintEncodeData` associated with the `singler_celltype_ontology` term | +| `blueprint_annotation_cl` | Name associated with the cell type ontology term in `singler_celltype_ontology` | | `consensus_ontology` | Cell type ontology term assigned as the consensus cell type | | `consensus_annotation` | Name associated with the assigned consensus cell type in `consensus_ontology` | diff --git a/analyses/cell-type-consensus/references/README.md b/analyses/cell-type-consensus/references/README.md index 2a494a9f7..b9e99d68b 100644 --- a/analyses/cell-type-consensus/references/README.md +++ b/analyses/cell-type-consensus/references/README.md @@ -42,6 +42,7 @@ The table includes the following columns: | `blueprint_ontology` | Cell type ontology term for `BlueprintEncodeData` cell type | | `blueprint_annotation_main` | Original name for the cell type as set by `BlueprintEncodeData` (main term) | | `blueprint_annotation_fine` | Original name for the cell type as set by `BlueprintEncodeData` (fine term) | +| `blueprint_annotation_cl` | Name for the cell type defined by [Cell Ontology](https://www.ebi.ac.uk/ols4/ontologies/cl) | | `consensus_ontology` | Cell type ontology term for consensus cell type | | `consensus_annotation` | Human readable name for the consensus cell type |