pdxnet-image-analysis-aacr2022/pdxnet-initialization.R at main · TheJacksonLaboratory/pdxnet-image-analysis-aacr2022 · GitHub

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base.dirs = list(
  "pdmr" = "/sbgenomics/project-files/PDMR_Image/",
  "pdmr-wgd" = "/sbgenomics/project-files/PDMR_Image/Datasets/Dataset_WGD/",
  "mda_pt_pdx_mouse_amg" = "/sbgenomics/project-files/PDTC-Image/MDA/Datasets/Dataset_PT_PDX_mouse_AMG/",
  "mda_tc_pt_pdx" = "/sbgenomics/project-files/PDTC-Image/MDA/Datasets/Dataset_TC_PT_PDX/",
  "mda-breast-pt-pdx" = "/sbgenomics/project-files/PDTC-Image/MDA/Datasets/Dataset_breast_PT_PDX/",
  "wustl" = "/sbgenomics/project-files/PDTC-Image/WUSTL/Datasets/Dataset_PDX/",
  "bcm-pdx-tif" = "/sbgenomics/project-files/PDTC-Image/BCM/Datasets/Dataset_PDX_TIF/",
  "bcm-pt-svs" = "/sbgenomics/project-files/PDTC-Image/BCM/Datasets/Dataset_PT_SVS/",
  "wistar-pt-pdx" = "/sbgenomics/project-files/PDTC-Image/WISTAR/Datasets/Dataset_PT_PDX/",
  "hci-pt-pdx" = "/sbgenomics/project-files/PDTC-Image/HCI/Datasets/Dataset_PT_PDX/",
  "pdmr-xtld" = '/sbgenomics/project-files/PDMR_Image/Datasets/Dataset_XTLD/',
  "jax-quarantine" = '/sbgenomics/project-files/External/JAX/Datasets/Dataset_Quarantine/'
)

source("pdxnet-initialization-base.R")


regional.annotation.dir <- "/sbgenomics/workspace/analysis/pdxnet-image-analysis-aacr2022/auxiliary/regional-annotations/"
json_cell_info_file <- "/sbgenomics/workspace/analysis/pdxnet-image-analysis-aacr2022/auxiliary/type_info.json"

regional.annotation.files <- list(
  "pdmr" = paste0(regional.annotation.dir, "pdmr-region-and-tissue-tile-labels.csv.gz"),
  "mda_tc_pt_pdx" = paste0(regional.annotation.dir, "mdacc-lung-region-and-tissue-tile-labels.csv.gz"),
  "mda_pt_pdx_mouse_amg" = paste0(regional.annotation.dir, "mdacc-mouse-region-and-tissue-tile-labels.csv.gz"),
  "bcm-pdx-tif" = paste0(regional.annotation.dir, "bcm-pdx-tif-region-and-tissue-tile-labels.csv.gz")
  # "bcm-pt-svs" = paste0(regional.annotation.dir, "bcm-pt-svs-region-and-tissue-tile-labels.csv.gz")
)

# bcm.pdx.tif.prefix <- "bcm-pdx-tif"
# bcm.pt.svs.prefix <- "bcm-pt-svs"
# hci.pt.pdx.prefix <- "hci-pt-pdx"
# mda.breast.pt.pdx.prefix <- "mda-breast-pt-pdx"
# wistar.pt.pdx.prefix <- "wistar-pt-pdx"