Atera Viz¶

In [1]:

import celldega as dega
import pandas as pd

import celldega as dega import pandas as pd

Visualize Xenium landscape in celldega¶

In [2]:

base_url = 'https://raw.githubusercontent.com/cornhundred/DegaFiles_WTA_Preview_FFPE_Breast_Cancer_outs/main'

base_url = 'https://raw.githubusercontent.com/cornhundred/DegaFiles_WTA_Preview_FFPE_Breast_Cancer_outs/main'

In [3]:

landscape = dega.viz.Landscape(
    technology='Xenium',
    base_url = base_url,
    max_tiles_to_view=25
)

landscape = dega.viz.Landscape( technology='Xenium', base_url = base_url, max_tiles_to_view=25 )

In [4]:

file_path = base_url + '/df_sig.parquet'
df_sig = pd.read_parquet(file_path)

file_path = base_url + '/df_sig.parquet' df_sig = pd.read_parquet(file_path)

In [5]:

df_sig.shape

df_sig.shape

Out[5]:

(18090, 34)

In [6]:

landscape

landscape

Out[6]:

In [7]:

mat = dega.clust.Matrix(data=df_sig)
mat.norm(axis='row', by='zscore')
mat.cluster()
cgm = dega.viz.Clustergram(matrix=mat, width=500, height=500)

mat = dega.clust.Matrix(data=df_sig) mat.norm(axis='row', by='zscore') mat.cluster() cgm = dega.viz.Clustergram(matrix=mat, width=500, height=500)

In [8]:

dega.viz.landscape_clustergram(landscape, cgm)

dega.viz.landscape_clustergram(landscape, cgm)

Out[8]: