vitessce example with scrnaseq and image #95

FADHLyemen · 2021-07-28T15:41:13Z

FADHLyemen
Jul 28, 2021

Hi Vitessce team,
I am interested to have one example combining scrna-seq and image.
I could not find it in
https://github.com/vitessce/vitessce-python/tree/master/docs/notebooks

I want to have something like:
http://vitessce.io/?dataset=linnarsson-2018&theme=dark

I am wondering on how to connect the h5ad with the image coordinates.

Thank you

Answered by FADHLyemen

Jul 30, 2021

@ilan-gold
what is file type for expression matrix

"type": "expression-matrix",
"fileType": "clusters.json",

https://github.com/vitessce/vitessce-data/tree/master/fake-files/output-expected/linnarsson
I try this code but still not working,

from vitessce import VitessceConfig, DataType as dt, FileType as ft

vc = VitessceConfig(name='linnarsson', description='Spatial organization of the somatosensory cortex revealed by osmFISH')
dataset = (
    vc.add_dataset(name='linnarsson')
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.cells.json",
        data_type=dt.CELLS,
        file_type=ft.CELLS_JSON,
    )
    .add_file(
        url="https://vitejson.s3.us-e…

View full answer

keller-mark · 2021-07-28T15:58:29Z

keller-mark
Jul 28, 2021
Maintainer

Hi @FADHLyemen,
There is a script here which demonstrates processing of an AnnData object containing an image file: https://github.com/vitessce/vitessce-python/blob/keller-mark/demo-data-processing/demos/human_lymph_node_10x_visium/src/create_zarr.py

It is not very well documented but may be helpful for you. The corresponding Vitessce configuration is here as raw JSON https://github.com/vitessce/vitessce/blob/8b07822f06da5e6d57d381c0633e7cd471cfbc7c/src/app/api.js#L77. We need to work on making a notebook which shows how to do configure it from Python.

2 replies

ilan-gold Jul 28, 2021
Maintainer

While the data is not public, here is an example of setting up a view configuration for a segmentation mask + image + AnnData container with quantification and clustering:

https://github.com/hubmapconsortium/portal-ui/blob/846d2b326af5e8eb46a5ef449bb3d651acdc64f5/context/app/api/vitessce_confs/base_confs.py#L363-L406

ilan-gold Jul 28, 2021
Maintainer

This is for the HuBMAP data portal but the data itself is not public yet.

The main differences between this and non-spatial data is the addition of "spatial" keys to the AnnDataWrapper like:
https://github.com/hubmapconsortium/portal-ui/blob/main/context/app/api/vitessce_confs/base_confs.py#L377

and the presence of pyramidal OME-TIFF images + segmentation files:
https://github.com/hubmapconsortium/portal-ui/blob/846d2b326af5e8eb46a5ef449bb3d651acdc64f5/context/app/api/vitessce_confs/base_confs.py#L398-L402

and then of course a SPATIAL component:
https://github.com/hubmapconsortium/portal-ui/blob/846d2b326af5e8eb46a5ef449bb3d651acdc64f5/context/app/api/vitessce_confs/base_confs.py#L409

FADHLyemen · 2021-07-29T14:17:46Z

FADHLyemen
Jul 29, 2021
Author

Thank you,
for the demo,
http://beta.vitessce.io/index.html?dataset=codeluppi-2018

could I download the data and run it locally using vitessce python?
Can I use any of your fake data to run it in my local vitessce or uplaod them to the s3 aws bucket?

0 replies

FADHLyemen · 2021-07-29T14:22:42Z

FADHLyemen
Jul 29, 2021
Author

for example for this demo
http://vitessce.io/?dataset=linnarsson-2018&theme=dark
the fake data is in:
https://github.com/vitessce/vitessce-data/tree/master/fake-files/input/linnarsson

but it has two h5ad files
I need to import them and do the same pipeline as in
https://github.com/vitessce/vitessce-python/blob/master/docs/notebooks/data_export_s3.ipynb

3 replies

ilan-gold Jul 29, 2021
Maintainer

@FADHLyemen The two files in there are hdf5 which are different than h5ad - a superset relationship, to be exact. h5ad is a wrapper around hdf5 files for saving AnnData objects to disk from their python representation. So all h5ad files are hdf5 but not vice-versa. Relatedly, AnnData can also be stored as zarr via the write_zarr method on an AnnData object.

FADHLyemen Jul 29, 2021
Author

@ilan-gold thank you for this.
so can I use this these two fake hdf5 to generate something in your demo:
http://vitessce.io/?dataset=linnarsson-2018&theme=dark

Maybe an easy way is to put my jason files in amazon s3 and paste them in vitessce app. maybe, we do not need the notebook example. I am trying to replicate your demo, so I can just replace your fake files with my similar files.

{
  "name": "Codeluppi et al., Nature Methods 2018",
  "description": "Spatial organization of the somatosensory cortex revealed by osmFISH",
  "version": "1.0.0",
  "initStrategy": "auto",
  "datasets": [
    {
      "uid": "codeluppi",
      "name": "Codeluppi",
      "files": [
        {
          "type": "cells",
          "fileType": "cells.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cells.json"
        },
        {
          "type": "cell-sets",
          "fileType": "cell-sets.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cell-sets.json"
        },
        {
          "type": "raster",
          "fileType": "raster.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.raster.json"
        },
        {
          "type": "molecules",
          "fileType": "molecules.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.molecules.json"
        },
        {
          "type": "neighborhoods",
          "fileType": "neighborhoods.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.neighborhoods.json"
        },
        {
          "type": "expression-matrix",
          "fileType": "clusters.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.clusters.json"
        }
      ]
    }
  ],
  "public": true,
  "coordinationSpace": {
    "embeddingZoom": {
      "PCA": 0,
      "TSNE": 0.75
    },
    "embeddingType": {
      "PCA": "PCA",
      "TSNE": "t-SNE"
    },
    "spatialZoom": {
      "A": -5.5
    },
    "spatialTargetX": {
      "A": 16000
    },
    "spatialTargetY": {
      "A": 20000
    }
  },
  "layout": [
    {
      "component": "description",
      "props": {
        "description": "Codeluppi et al., Nature Methods 2018: Spatial organization of the somatosensory cortex revealed by osmFISH"
      },
      "x": 0,
      "y": 0,
      "w": 2,
      "h": 1
    },
    {
      "component": "layerController",
      "x": 0,
      "y": 1,
      "w": 2,
      "h": 4
    },
    {
      "component": "status",
      "x": 0,
      "y": 5,
      "w": 2,
      "h": 1
    },
    {
      "component": "spatial",
      "coordinationScopes": {
        "spatialZoom": "A",
        "spatialTargetX": "A",
        "spatialTargetY": "A"
      },
      "x": 2,
      "y": 0,
      "w": 4,
      "h": 4
    },
    {
      "component": "genes",
      "x": 9,
      "y": 0,
      "w": 3,
      "h": 2
    },
    {
      "component": "cellSets",
      "x": 9,
      "y": 3,
      "w": 3,
      "h": 2
    },
    {
      "component": "heatmap",
      "props": {
        "transpose": true
      },
      "x": 2,
      "y": 4,
      "w": 5,
      "h": 2
    },
    {
      "component": "cellSetExpression",
      "x": 7,
      "y": 4,
      "w": 5,
      "h": 2
    },
    {
      "component": "scatterplot",
      "coordinationScopes": {
        "embeddingType": "PCA",
        "embeddingZoom": "PCA"
      },
      "x": 6,
      "y": 0,
      "w": 3,
      "h": 2
    },
    {
      "component": "scatterplot",
      "coordinationScopes": {
        "embeddingType": "TSNE",
        "embeddingZoom": "TSNE"
      },
      "x": 6,
      "y": 2,
      "w": 3,
      "h": 2
    }
  ]
}

ilan-gold Jul 29, 2021
Maintainer

@FADHLyemen Those files are fake files in that they contain much fewer data points/data than the actual demo. If you want to replicate the demo, it's probably best to actually run the scripts in vitessce-data to generate the data, then you can proceed as you said, putting the generated data on the cloud and then replacing the URL's in the view configuration.

FADHLyemen · 2021-07-29T18:27:57Z

FADHLyemen
Jul 29, 2021
Author

@ilan-gold
when you said, run the scripts, do you mean this https://github.com/vitessce/vitessce-data/blob/master/scripts/process_linnarsson.sh

second, I already have the expected files as JSON format:
https://github.com/vitessce/vitessce-data/tree/master/fake-files/output-expected/linnarsson

I am trying to think how to replicate what I did with you in
https://github.com/vitessce/vitessce-python/blob/master/docs/notebooks/data_export_s3.ipynb

and which code I should replace the below one to run these json files?

vc = VitessceConfig(name='Habib et al', description='COVID-19 Healthy Donor Brain')
dataset = vc.add_dataset(name='Brain').add_object(AnnDataWrapper(
        adata,
        mappings_obsm=["X_umap"],
        mappings_obsm_names=["UMAP"],
        cell_set_obs=["CellType"],
        cell_set_obs_names=["Cell Type"],
        expression_matrix="X",
        matrix_gene_var_filter="top_highly_variable"
))
scatterplot = vc.add_view(dataset, cm.SCATTERPLOT, mapping="UMAP")
cell_sets = vc.add_view(dataset, cm.CELL_SETS)
genes = vc.add_view(dataset, cm.GENES)
heatmap = vc.add_view(dataset, cm.HEATMAP)
vc.layout((scatterplot | (cell_sets / genes)) / heatmap);

s3 = boto3.resource(
    service_name='s3',
    aws_access_key_id=os.environ['VITESSCE_S3_ACCESS_KEY_ID'],
    aws_secret_access_key=os.environ['VITESSCE_S3_SECRET_ACCESS_KEY'],
)

3 replies

keller-mark Jul 29, 2021
Maintainer

If you have files in the JSON formats supported by Vitessce, you can replace the .add_object() function with .add_file() (see documentation here).

Like this:

from vitessce import VitessceConfig, DataType as dt, FileType as ft

vc = VitessceConfig(name='', description='')
dataset = (
    vc.add_dataset(name='Brain')
    .add_file(
        url="http://example.com/cells.json",
        data_type=dt.CELLS,
        file_type=ft.CELLS_JSON,
    )
    .add_file(
        url="http://example.com/molecules.json",
        data_type=dt.MOLECULES,
        file_type=ft.MOLECULES_JSON,
    )
)

keller-mark Jul 29, 2021
Maintainer

The data types and file types are defined here: https://vitessce.github.io/vitessce-python/api_config.html#vitessce.constants.DataType

keller-mark Jul 29, 2021
Maintainer

Note that data added to the configuration via .add_file is not included in the upload when running the vc.export() function.

FADHLyemen · 2021-07-30T03:59:55Z

FADHLyemen
Jul 30, 2021
Author

@ilan-gold
what is file type for expression matrix

"type": "expression-matrix",
"fileType": "clusters.json",

https://github.com/vitessce/vitessce-data/tree/master/fake-files/output-expected/linnarsson
I try this code but still not working,

from vitessce import VitessceConfig, DataType as dt, FileType as ft

vc = VitessceConfig(name='linnarsson', description='Spatial organization of the somatosensory cortex revealed by osmFISH')
dataset = (
    vc.add_dataset(name='linnarsson')
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.cells.json",
        data_type=dt.CELLS,
        file_type=ft.CELLS_JSON,
    )
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.molecules.json",
        data_type=dt.MOLECULES,
        file_type=ft.MOLECULES_JSON,
    )
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.cell-sets.json",
        data_type=dt.CELL_SETS,
        file_type=ft.CELL_SETS_JSON,
    )
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.raster.json",
        data_type=dt.RASTER,
        file_type=ft.RASTER_JSON,
    )
     .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.neighborhoods.json",
        data_type=dt.NEIGHBORHOODS,
        file_type=ft.NEIGHBORHOODS_JSON,
    )
    .add_file(
        url="https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.clusters.json",
        data_type=dt.EXPRESSION_MATRIX,
        file_type=ft.ANNDATA_CELLS_ZARR,
    )
)

scatterplot = vc.add_view(dataset, cm.SCATTERPLOT, mapping="t-SNE")
cell_sets = vc.add_view(dataset, cm.CELL_SETS)
genes = vc.add_view(dataset, cm.GENES)
heatmap = vc.add_view(dataset, cm.HEATMAP)
vc.layout((scatterplot | (cell_sets / genes)) / heatmap);


s3 = boto3.resource(
    service_name='s3',
    aws_access_key_id='Advdfvdfvdfvd',
    aws_secret_access_key='vfvfddddddddddddddddddddddddddddddddd',
)

config_dict = vc.export(to='S3', s3=s3, bucket_name='vitejson')


vitessce_url = "http://vitessce.io/?url=data:," + quote_plus(json.dumps(config_dict))
vitessce_url

http://vitessce.io/?url=data:,%7B%22version%22%3A+%221.0.2%22%2C+%22name%22%3A+%22linnarsson%22%2C+%22description%22%3A+%22Spatial+organization+of+the+somatosensory+cortex+revealed+by+osmFISH%22%2C+%22datasets%22%3A+%5B%7B%22uid%22%3A+%22A%22%2C+%22name%22%3A+%22linnarsson%22%2C+%22files%22%3A+%5B%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.cells.json%22%2C+%22type%22%3A+%22cells%22%2C+%22fileType%22%3A+%22cells.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.molecules.json%22%2C+%22type%22%3A+%22molecules%22%2C+%22fileType%22%3A+%22molecules.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.cell-sets.json%22%2C+%22type%22%3A+%22cell-sets%22%2C+%22fileType%22%3A+%22cell-sets.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.raster.json%22%2C+%22type%22%3A+%22raster%22%2C+%22fileType%22%3A+%22raster.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.neighborhoods.json%22%2C+%22type%22%3A+%22neighborhoods%22%2C+%22fileType%22%3A+%22neighborhoods.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.clusters.json%22%2C+%22type%22%3A+%22expression-matrix%22%2C+%22fileType%22%3A+%22anndata-cells.zarr%22%7D%5D%7D%5D%2C+%22coordinationSpace%22%3A+%7B%22dataset%22%3A+%7B%22A%22%3A+%22A%22%7D%2C+%22embeddingType%22%3A+%7B%22A%22%3A+%22t-SNE%22%7D%7D%2C+%22layout%22%3A+%5B%7B%22component%22%3A+%22scatterplot%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%2C+%22embeddingType%22%3A+%22A%22%7D%2C+%22x%22%3A+0.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+6.0%7D%2C+%7B%22component%22%3A+%22cellSets%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22genes%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+3.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22heatmap%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+0%2C+%22y%22%3A+6.0%2C+%22w%22%3A+12%2C+%22h%22%3A+6.0%7D%5D%2C+%22initStrategy%22%3A+%22auto%22%7D

14 replies

FADHLyemen Aug 2, 2021
Author

I can easy access the json files from the links:
https://vitejson.s3.us-east-2.amazonaws.com/linnarsson.cells.json

FADHLyemen Aug 2, 2021
Author

http://vitessce.io/?url=data:,%7B%22version%22%3A+%221.0.2%22%2C+%22name%22%3A+%22linnarsson%22%2C+%22description%22%3A+%22Spatial+organization+of+the+somatosensory+cortex+revealed+by+osmFISH%22%2C+%22datasets%22%3A+%5B%7B%22uid%22%3A+%22A%22%2C+%22name%22%3A+%22linnarsson%22%2C+%22files%22%3A+%5B%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.cells.json%22%2C+%22type%22%3A+%22cells%22%2C+%22fileType%22%3A+%22cells.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.molecules.json%22%2C+%22type%22%3A+%22molecules%22%2C+%22fileType%22%3A+%22molecules.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.cell-sets.json%22%2C+%22type%22%3A+%22cell-sets%22%2C+%22fileType%22%3A+%22cell-sets.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.raster.json%22%2C+%22type%22%3A+%22raster%22%2C+%22fileType%22%3A+%22raster.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.neighborhoods.json%22%2C+%22type%22%3A+%22neighborhoods%22%2C+%22fileType%22%3A+%22neighborhoods.json%22%7D%2C+%7B%22url%22%3A+%22https%3A%2F%2Fvitejson.s3.us-east-2.amazonaws.com%2Flinnarsson.clusters.json%22%2C+%22type%22%3A+%22expression-matrix%22%2C+%22fileType%22%3A+%22clusters.json%22%7D%5D%7D%5D%2C+%22coordinationSpace%22%3A+%7B%22dataset%22%3A+%7B%22A%22%3A+%22A%22%7D%2C+%22embeddingType%22%3A+%7B%22A%22%3A+%22t-SNE%22%7D%7D%2C+%22layout%22%3A+%5B%7B%22component%22%3A+%22scatterplot%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%2C+%22embeddingType%22%3A+%22A%22%7D%2C+%22x%22%3A+0.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+3.0%2C+%22h%22%3A+6.0%7D%2C+%7B%22component%22%3A+%22cellSets%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+3.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+3.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22genes%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+3.0%2C+%22y%22%3A+3.0%2C+%22w%22%3A+3.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22heatmap%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+0.0%2C+%22y%22%3A+6.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+6.0%7D%2C+%7B%22component%22%3A+%22spatial%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+12%7D%5D%2C+%22initStrategy%22%3A+%22auto%22%7D

ilan-gold Aug 2, 2021
Maintainer

@FADHLyemen Accessing the data as a URL is the same as downloading. It seems like CORS are misconfigured, if I had to guess. Please see this to be sure.

FADHLyemen Aug 2, 2021
Author

@ilan-gold
It finally works after adding the below lines, thank you for your patient @ilan-gold

[
  {
    "AllowedHeaders": ["*"],
    "AllowedMethods": ["GET"],
    "AllowedOrigins": ["*"],
    "ExposeHeaders": ["Content-Range"],
    "MaxAgeSeconds": 3000
  }
]

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