{
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    {
      "cell_type": "code",
      "execution_count": null,
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      "source": [
        "%matplotlib inline"
      ]
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      "source": [
        "\nSpatially resolved, highly multiplexed RNA profiling in single cells\n============================================================================================\n\nRongqin Ke, Marco Mignardi, Alexandra Pacureanu, Jessica Svedlund, Johan Botling, Carolina W\u00e4hlby,\nMats Nilsson\n\nThis publication can be found at https://science.sciencemag.org/content/348/6233/aaa6090 and the\ndata referenced below can be downloaded from\n\nChecklist:\n- [x] point locations\n- [ ] cell locations\n- [ ] cell x gene expression matrix (derivable)\n\nLoad the data\n-------------\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import requests\nfrom io import BytesIO\n\nimport pandas as pd\n\nimport starspace\nfrom starspace.constants import *\n\nresponse = requests.get(\n    \"https://d24h2xsgaj29mf.cloudfront.net/raw/iss_ke_2013_nat-methods_breast-cancer/all_spots.csv\"\n)\n\ndata = pd.read_csv(BytesIO(response.content))\n\ncolumn_map = {\n    \"gene\": SPOTS_REQUIRED_VARIABLES.GENE_NAME.value,\n    \"x\": SPOTS_REQUIRED_VARIABLES.X_SPOT.value,\n    \"y\": SPOTS_REQUIRED_VARIABLES.Y_SPOT.value,\n    \"qual\": SPOTS_OPTIONAL_VARIABLES.QUALITY.value,\n    \"fov\": SPOTS_OPTIONAL_VARIABLES.FIELD_OF_VIEW.value,\n    \"gene_code\": \"gene_code\",\n    \"barcode\": \"barcode\",\n}\n\nauthors = [\n    \"Rongqin Ke\", \"Marco Mignardi\", \"Alexandra Pacureanu\", \"Jessica Svedlund\", \"Johan Botling\",\n    \"Carolina W\u00e4hlby\", \"Mats Nilsson\"\n]\nattributes = {\n    REQUIRED_ATTRIBUTES.ASSAY: ASSAYS.ISS,\n    REQUIRED_ATTRIBUTES.SAMPLE_TYPE: \"Her2+ breast carcinoma\",\n    REQUIRED_ATTRIBUTES.AUTHORS: authors,\n    REQUIRED_ATTRIBUTES.YEAR: 2013,\n    REQUIRED_ATTRIBUTES.ORGANISM: \"human\",\n    OPTIONAL_ATTRIBUTES.PUBLICATION_NAME: (\n        \"In situ sequencing for RNA analysis in preserved tissue and cells\"\n    ),\n    OPTIONAL_ATTRIBUTES.PUBLICATION_URL: \"https://www.nature.com/articles/nmeth.2563\",\n}\n\nstandard_columns = [column_map[c] for c in data.columns]\ndata.columns = standard_columns\n\nspots = starspace.Spots.from_spot_data(data, attributes)\n\n# s3_url = \"s3://starfish.data.output-warehouse/iss_ke_2013_nat-methods_breast-cancer\"\nlocal_url = \"iss_ke_2013_nat-methods_breast-cancer/\"\nspots.save_zarr(local_url)"
      ]
    }
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