Landscape-Matrix Xenium¶

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 [8]:

import pandas as pd
import celldega as dega

import pandas as pd import celldega as dega

iST Landscape View¶

In [9]:

base_url = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_Prime_Human_Skin_FFPE_outs/main/Xenium_Prime_Human_Skin_FFPE_outs'

base_url = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_Prime_Human_Skin_FFPE_outs/main/Xenium_Prime_Human_Skin_FFPE_outs'

Make Landscape Widget

In [10]:

landscape_ist = dega.viz.Landscape(
    technology='Xenium',
    ini_zoom = -4.5,
    ini_x=6000,
    ini_y=8000,
    base_url = base_url,
    height = 700,
    width= 600
)

landscape_ist = dega.viz.Landscape( technology='Xenium', ini_zoom = -4.5, ini_x=6000, ini_y=8000, base_url = base_url, height = 700, width= 600 )

Make Matrix widget

In [11]:

file_path = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_Prime_Human_Skin_FFPE_outs/main/Xenium_Prime_Human_Skin_FFPE_outs/df_sig.parquet'
df = pd.read_parquet(file_path)
network = dega.clust.hc(df)
mat = dega.viz.Matrix(network=network, width=500, height=500)

file_path = 'https://raw.githubusercontent.com/broadinstitute/celldega_Xenium_Prime_Human_Skin_FFPE_outs/main/Xenium_Prime_Human_Skin_FFPE_outs/df_sig.parquet' df = pd.read_parquet(file_path) network = dega.clust.hc(df) mat = dega.viz.Matrix(network=network, width=500, height=500)

Landscape-Matrix View¶

In [12]:

dega.viz.landscape_matrix(landscape_ist, mat)

dega.viz.landscape_matrix(landscape_ist, mat)

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