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pdxnet-initialization-base.R
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136 lines (126 loc) · 9.98 KB
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mask_area_files <-
list("mda_pt_pdx_mouse_amg" = paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], 'histoqc/histoqc_output_mda_pt_pdx_mouse_amg_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/mda_pt_pdx_mouse_amg-mask-area.csv'),
"mda_tc_pt_pdx" = paste0(base.dirs[["mda_tc_pt_pdx"]], '/histoqc_output_mda_tc_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/mda_tc_pt_pdx-mask-area.csv'),
"pdmr" = paste0(base.dirs[["pdmr"]], 'histoqc/aggregate/mask_area/pdmr-mask-area.csv'),
"pdmr-wgd" = paste0(base.dirs[["pdmr-wgd"]], 'histoqc/aggregate/mask_area/pdmr-wgd-mask-area.csv'),
"wustl" = paste0(base.dirs[["wustl"]], 'histoqc/aggregate/mask_area/wustl-mask-area.csv'),
"bcm-pdx-tif" = paste0(base.dirs[["bcm-pdx-tif"]], 'histoqc/histoqc_output_bcm_pdx_tif_all_v2.1-bcm-pdx-tif/mask_area/bcm-pdx-tif-mask-area.csv'),
"bcm-pt-svs" = paste0(base.dirs[["bcm-pt-svs"]], 'histoqc/histoqc_output_bcm_pt_svs_all_v2.1-bcm-pt-svs/mask_area/bcm-pt-svs-mask-area.csv'),
"hci-pt-pdx" = paste0(base.dirs[["hci-pt-pdx"]], 'histoqc/histoqc_output_hci_adjusted_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/hci-pt-pdx-mask-area.csv'),
"mda-breast-pt-pdx" = paste0(base.dirs[["mda-breast-pt-pdx"]], 'histoqc/histoqc_output_mda_breast_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/mda-breast-pt-pdx-mask-area.csv'),
"wistar-pt-pdx" = paste0(base.dirs[["wistar-pt-pdx"]], 'histoqc/histoqc_output_wistar_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/wistar-pt-pdx-mask-area.csv'),
"pdmr-xtld" = paste0(base.dirs[["pdmr-xtld"]], 'histoqc/histoqc_output_pdmr_xtld_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/pdmr-xtld-mask-area.csv'),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], 'histoqc/histoqc_output_jax-no-blur-no-fat-no-cover-no-pen/mask_area/jax-quarantine-mask-area.csv')
)
dataset.names <-
list("mda_pt_pdx_mouse_amg" = "MDACC (Lung 1)",
"mda_tc_pt_pdx" = "MDACC (Lung 2)",
"pdmr" = "PDMR",
"wustl" = "WUSTL",
"bcm-pdx-tif" = "BCM (PDX)",
"bcm-pt-svs" = "BCM",
"hci-pt-pdx" = "HCI",
"mda-breast-pt-pdx" = "MDACC (Breast)",
"wistar-pt-pdx" = "WISTAR"
)
mask_area_dirs <-
list("mda_pt_pdx_mouse_amg" = paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], 'histoqc/histoqc_output_mda_pt_pdx_mouse_amg_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"mda_tc_pt_pdx" = paste0(base.dirs[["mda_tc_pt_pdx"]], '/histoqc_output_mda_tc_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"pdmr" = paste0(base.dirs[["pdmr"]], 'histoqc/aggregate/mask_area/'),
"pdmr-wgd" = paste0(base.dirs[["pdmr-wgd"]], 'histoqc/aggregate/mask_area/'),
"wustl" = paste0(base.dirs[["wustl"]], 'histoqc/aggregate/mask_area/'),
"bcm-pdx-tif" = paste0(base.dirs[["bcm-pdx-tif"]], 'histoqc/histoqc_output_bcm_pdx_tif_all_v2.1-bcm-pdx-tif/mask_area/'),
"bcm-pt-svs" = paste0(base.dirs[["bcm-pt-svs"]], 'histoqc/histoqc_output_bcm_pt_svs_all_v2.1-bcm-pt-svs/mask_area/'),
"hci-pt-pdx" = paste0(base.dirs[["hci-pt-pdx"]], 'histoqc/histoqc_output_hci_adjusted_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"mda-breast-pt-pdx" = paste0(base.dirs[["mda-breast-pt-pdx"]], 'histoqc/histoqc_output_mda_breast_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"wistar-pt-pdx" = paste0(base.dirs[["wistar-pt-pdx"]], 'histoqc/histoqc_output_wistar_all_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"pdmr-xtld" = paste0(base.dirs[["pdmr-xtld"]], 'histoqc/histoqc_output_pdmr_xtld_v2.1-no-blur-no-fat-no-cover-no-pen/mask_area/'),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], 'histoqc/histoqc_output_jax-no-blur-no-fat-no-cover-no-pen/mask_area/')
)
original.image.resolutions <-
list("mda_pt_pdx_mouse_amg" = 20,
"mda_tc_pt_pdx" = 20,
"pdmr" = 20,
"pdmr-wgd" = 20,
"wustl" = 40,
"bcm-pdx-tif" = 20,
"bcm-pt-svs" = 20,
"hci-pt-pdx" = 20,
"mda-breast-pt-pdx" = 20,
"wistar-pt-pdx" = 40
)
histoqc_dirs <-
list("mda_pt_pdx_mouse_amg" = paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], 'histoqc/histoqc_output_mda_pt_pdx_mouse_amg_all_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"mda_tc_pt_pdx" = paste0(base.dirs[["mda_tc_pt_pdx"]], '/histoqc_output_mda_tc_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"pdmr" = paste0(base.dirs[["pdmr"]], 'histoqc/aggregate/'),
"pdmr-unmarked" = paste0(base.dirs[["pdmr"]], 'histoqc/histoqc_output_pdmr_unmarked_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"pdmr-marked" = paste0(base.dirs[["pdmr"]], 'histoqc/histoqc_output_pdmr_marked_v2.1-no-blur-no-fat-no-cover-with-pen/'),
"pdmr-wgd-unmarked" = paste0(base.dirs[["pdmr-wgd"]], 'histoqc/histoqc_output_pdmr_wgd_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"pdmr-wgd-marked" = paste0(base.dirs[["pdmr-wgd"]], 'histoqc/histoqc_output_pdmr_wgd_v2.1-no-blur-no-fat-no-cover-with-pen/'),
"pdmr-wgd" = paste0(base.dirs[["pdmr-wgd"]], 'histoqc/aggregate/'),
"wustl" = paste0(base.dirs[["wustl"]], 'histoqc/aggregate/'),
"bcm-pdx-tif" = paste0(base.dirs[["bcm-pdx-tif"]], 'histoqc/histoqc_output_bcm_pdx_tif_all_v2.1-bcm-pdx-tif/'),
"bcm-pt-svs" = paste0(base.dirs[["bcm-pt-svs"]], 'histoqc/histoqc_output_bcm_pt_svs_all_v2.1-bcm-pt-svs/'),
"hci-pt-pdx" = paste0(base.dirs[["hci-pt-pdx"]], 'histoqc/histoqc_output_hci_adjusted_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"mda-breast-pt-pdx" = paste0(base.dirs[["mda-breast-pt-pdx"]], 'histoqc/histoqc_output_mda_breast_pt_pdx_all_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"wistar-pt-pdx" = paste0(base.dirs[["wistar-pt-pdx"]], 'histoqc/histoqc_output_wistar_all_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"pdmr-xtld" = paste0(base.dirs[["pdmr-xtld"]], 'histoqc/histoqc_output_pdmr_xtld_v2.1-no-blur-no-fat-no-cover-no-pen/'),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], 'histoqc/histoqc_output_jax-no-blur-no-fat-no-cover-no-pen/')
)
metadata.files = list(
"pdmr"= paste0(base.dirs[["pdmr"]], "Metadata/PDXNETimage_metadata_pdmr_standardized.xlsx"),
"pdmr-wgd"= paste0(base.dirs[["pdmr-wgd"]], "Metadata/PDXNETimage_metadata_pdmr_wgd_standardized.xlsx"),
"mda_pt_pdx_mouse_amg"= paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], "Metadata/PDXimage032021_MDACClung2_BF_standardized V2.xlsx"),
"mda_tc_pt_pdx"= paste0(base.dirs[["mda_tc_pt_pdx"]], "Metadata/PDXNETimage_metadataMDACCbf_lung1_standardized.xlsx"),
"mda-breast-pt-pdx"= paste0(base.dirs[["mda-breast-pt-pdx"]], "Metadata/Raso_Meric_Breast_Images_MDACC_standardized.xlsx"),
"wustl"= paste0(base.dirs[["wustl"]], "Metadata/PDXNETimage_metadata_wustl_all_standardized.RJM_220726.xlsx"),
"bcm-pdx-tif"= paste0(base.dirs[["bcm-pdx-tif"]], "Metadata/PDXNETimage_metadata_bcm_pdx_tif_standardized.xlsx"),
"bcm-pt-svs"= paste0(base.dirs[["bcm-pt-svs"]], "Metadata/PDXNETimage_metadata_bcm_pt_svs_standardized.xlsx"),
"wistar-pt-pdx"= paste0(base.dirs[["wistar-pt-pdx"]], "Metadata/PDXNETimage_metadata_wistar_standardized.xlsx"),
"hci-pt-pdx"= paste0(base.dirs[["hci-pt-pdx"]], "Metadata/PDXNETimage_metadata_HCI_20x_standardized.xlsx"),
"pdmr-xtld"= paste0(base.dirs[["pdmr-xtld"]], "Metadata/PDXNETimage_metadata_pdmr_xtld_standardized.xlsx"),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], "Metadata/PDXNETimage_metadata_jax_quarantine.xlsx")
# "jax-quarantine" = '/sbgenomics/workspace/PDXNETimage_metadata_jax_quarantine.xlsx'
)
hovernet_centroid_dirs <-
list("mda_pt_pdx_mouse_amg" = paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], 'Hovernet/slide_cell_summary/'),
"mda_tc_pt_pdx" = paste0(base.dirs[["mda_tc_pt_pdx"]], 'Hovernet/slide_cell_summary/'),
"pdmr" = paste0(base.dirs[["pdmr"]], 'Hovernet/slide_cell_summary/'),
"pdmr-wgd" = paste0(base.dirs[["pdmr-wgd"]], 'Hovernet/slide_cell_summary/'),
"wustl" = paste0(base.dirs[["wustl"]], 'Hovernet/slide_cell_summary/'),
"bcm-pdx-tif" = paste0(base.dirs[["bcm-pdx-tif"]], 'Hovernet/slide_cell_summary/'),
"bcm-pt-svs" = paste0(base.dirs[["bcm-pt-svs"]], 'Hovernet/slide_cell_summary/'),
"hci-pt-pdx" = paste0(base.dirs[["hci-pt-pdx"]], 'Hovernet/slide_cell_summary/'),
"mda-breast-pt-pdx" = paste0(base.dirs[["mda-breast-pt-pdx"]], 'Hovernet/slide_cell_summary/'),
"wistar-pt-pdx" = paste0(base.dirs[["wistar-pt-pdx"]], 'Hovernet/slide_cell_summary/'),
"pdmr-xtld" = paste0(base.dirs[["pdmr-xtld"]], 'Hovernet/slide_cell_summary/'),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], 'Hovernet/slide_cell_summary/')
)
image.metadata.files = list(
"pdmr"= paste0(base.dirs[["pdmr"]], "metadata/pdmr-svs-metadata.csv"),
"pdmr-wgd" = paste0(base.dirs[["pdmr-wgd"]], "metadata/pdmr-wgd-svs-metadata.csv"),
"mda_pt_pdx_mouse_amg"= paste0(base.dirs[["mda_pt_pdx_mouse_amg"]], "metadata/mda_pt_pdx_mouse_amg-svs-metadata.csv"),
"mda_tc_pt_pdx"= paste0(base.dirs[["mda_tc_pt_pdx"]], "metadata/mda_tc_pt_pdx-svs-metadata.csv"),
"mda-breast-pt-pdx"= paste0(base.dirs[["mda-breast-pt-pdx"]], "metadata/mda-breast-pt-pdx-svs-metadata.csv"),
"wustl"= paste0(base.dirs[["wustl"]], "metadata/wustl-svs-metadata.csv"),
"bcm-pdx-tif"= paste0(base.dirs[["bcm-pdx-tif"]], "metadata/bcm-pdx-tif-svs-metadata.csv"),
"bcm-pt-svs"= paste0(base.dirs[["bcm-pt-svs"]], "metadata/bcm-pt-svs-svs-metadata.csv"),
"wistar-pt-pdx"= paste0(base.dirs[["wistar-pt-pdx"]], "metadata/wistar-pt-pdx-svs-metadata.csv"),
"hci-pt-pdx"= paste0(base.dirs[["hci-pt-pdx"]], "metadata/hci-pt-pdx-svs-metadata.csv"),
"pdmr-xtld"= paste0(base.dirs[["pdmr-xtld"]], "metadata/pdmr-xtld-svs-metadata.csv"),
"jax-quarantine" = paste0(base.dirs[["jax-quarantine"]], "metadata/jax-quarantine-svs-metadata.csv")
)
sites = list(
"pdmr" = "PDMR",
"pdmr-wgd" = "PDMR",
"mda_pt_pdx_mouse_amg" = "MDACC",
"mda_tc_pt_pdx"= "MDACC",
"mda-breast-pt-pdx" = "MDACC",
"wustl" = "WUSTL",
"bcm-pdx-tif" = "BCM",
"bcm-pt-svs" = "BCM",
"wistar-pt-pdx" = "WISTAR",
"hci-pt-pdx" = "HCI",
"pdmr-xtld" = "PDMR",
"jax-quarantine" = "JAX"
)