Examples: Visium Brain

The test data file locates at https://github.com/bioinfo-biols/RidgeSpace/tree/main/tests/test.h5ad.

[1]:

import RidgeSpace
import anndata as ad
import seaborn as sns
sns.set(style="ticks", font_scale=1.5)
adata = ad.read_h5ad('./tests/test.h5ad')

Preproccess

Only need run once.

[2]:

RidgeSpace.tl_mesh(adata, mesh_optimization=True, save_address='test')

Radius   Count
366.531036    2322
365.005479    1946
365.001370    1910
366.772409    1760
367.266933     807
dtype: int64
Use default radius 373.8616562312856
Triangles mesh saved in ./Ridge_tmp/test/
Mesh optimization done

[3]:

RidgeSpace.tl_HE(adata, save_address='test', filter_background=True, threshold_scale= 1.1)

Using CytAssist_FreshFrozen_Mouse_Brain
HE information saved in ./Ridge_tmp/test/

Denoising for each gene for ploting later. Only need run once.

[4]:

RidgeSpace.tl_denoise(adata, plot_name = 'Mbp', save_address='test')

Denoised value for Mbp saved in ./Ridge_tmp/test/

[5]:

RidgeSpace.tl_denoise(adata, plot_name = 'Tnnt1', save_address='test')

Denoised value for Tnnt1 saved in ./Ridge_tmp/test/

[6]:

RidgeSpace.tl_denoise(adata, plot_name = 'Tnnt2', save_address='test')

Denoised value for Tnnt2 saved in ./Ridge_tmp/test/

[7]:

RidgeSpace.tl_denoise(adata, plot_name = 'Baiap2', save_address='test')

Denoised value for Baiap2 saved in ./Ridge_tmp/test/

[8]:

RidgeSpace.tl_denoise(adata, plot_name = 'Baiap3', save_address='test')

Denoised value for Baiap3 saved in ./Ridge_tmp/test/

Single gene

Close view

[6]:

RidgeSpace.pl_single(adata, plot_name = 'Mbp', obs_cluster='Clusters', save_address='test', elev=40, view=160, lw=1, normalize_z=True, return_ax=True)

[6]:

<Axes3DSubplot:xlabel='Spatial 1', ylabel='Spatial 2'>

Distant view

[5]:

RidgeSpace.pl_single(adata, plot_name = 'Mbp', obs_cluster='Clusters', save_address='test', elev=60, view=160, bg_alpha=5, normalize_z=True, return_ax=True)

[5]:

<Axes3DSubplot:xlabel='Spatial 1', ylabel='Spatial 2'>

Overlay Histology

[9]:

RidgeSpace.pl_single(adata, plot_name = 'Mbp', obs_cluster='Clusters', save_address='test', elev=30, view=160,\
                     plot_HE=True, plot_clustering=True, clustering_alpha=0.2)

Multiple genes

[10]:

RidgeSpace.pl_multipleOUT(adata, plot_nameA = 'Tnnt1', plot_nameB = 'Tnnt2', obs_cluster='Clusters', normalize_z=True, save_address='test', \
                         elev=20, view=160, plot_HE=True, z_height=1.5, lw=1, select_c=['#aa40fc', '#8e584d', '#b0c9ea', '#ff8110', '#2179b6', '#29a06a'])

[14]:

RidgeSpace.pl_multipleOUT(adata, plot_nameA = 'Tnnt2', plot_nameB = 'Tnnt1', obs_cluster='Clusters', normalize_z=True, normlabels=False, save_address='test',\
                          elev=20, view=160, plot_HE=True, bg_alphaA=1, z_height=1.5, lw=1, select_c=['#aa40fc', '#8e584d', '#b0c9ea', '#ff8110', '#2179b6', '#29a06a'])

[16]:

RidgeSpace.pl_multipleIN(adata, plot_nameA = 'Baiap3', plot_nameB = 'Baiap2', obs_cluster='Clusters', save_address='test',\
                         normlabels=False, elev=20, view=10, height=120, plot_HE=True, HE_slice=4, plot_clustering=True, clustering_alpha=0.2, lw=1, ylim_min=800)

Trajectory

[17]:

RidgeSpace.pl_trajectory(adata, plot_name = 'Pseudotime', obs_cluster='Clusters', elev=45, view=165, HE_z=10, save_address='test',\
                min_length=0.2, density_arrow=0.3, lw_arrow=1.2, zlim_min=0, xlim_min=1000, ylim_min=1000)

No file named Pseudotime in ./Ridge_tmp/test/
Using noisy information in adata