Yearbook Query¶

In [1]:

%load_ext autoreload
%autoreload 2
%env ANYWIDGET_HMR=1

%load_ext autoreload %autoreload 2 %env ANYWIDGET_HMR=1

env: ANYWIDGET_HMR=1

In [2]:

import celldega as dega

import celldega as dega

/Users/feni/Documents/celldega/dega/lib/python3.12/site-packages/h5py/__init__.py:36: UserWarning: h5py is running against HDF5 1.14.5 when it was built against 1.14.6, this may cause problems
  _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
/Users/feni/Documents/celldega/dega/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.
  warnings.warn(
/Users/feni/Documents/celldega/dega/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import DistributionNotFound, get_distribution
/Users/feni/Documents/celldega/dega/lib/python3.12/site-packages/anndata/__init__.py:44: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)

In [3]:

base_url = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs/main/Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs'

base_url = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs/main/Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs'

In [4]:

dega.viz.Landscape(
    technology='Xenium', 
    base_url = base_url
)

dega.viz.Landscape( technology='Xenium', base_url = base_url )

Out[4]:

In [5]:

yb = dega.viz.Yearbook(
    base_url=base_url,
    rows=3,
    cols=6,
    portrait_size_um=20
)
yb

yb = dega.viz.Yearbook( base_url=base_url, rows=3, cols=6, portrait_size_um=20 ) yb

Out[5]:

In [ ]: