Figure 4a, b, c#

[1]:

%load_ext nb_black

import scdiffeq_analyses as sdq_an
import scdiffeq as sdq
import cellplots as cp
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import anndata
import larry
import glob

/home/mvinyard/.anaconda3/envs/sdq/lib/python3.9/site-packages/torch/cuda/__init__.py:611: UserWarning: Can't initialize NVML
  warnings.warn("Can't initialize NVML")

[2]:

adata_ref = sdq.io.read_h5ad(
    "/home/mvinyard/data/adata.reprocessed_19OCT2023.more_feature_inclusive.h5ad"
)
umap_model = sdq.io.read_pickle("/home/mvinyard/data/umap_model.pkl")

AnnData object with n_obs × n_vars = 130887 × 2492
    obs: 'Library', 'Cell barcode', 'Time point', 'Starting population', 'Cell type annotation', 'Well', 'SPRING-x', 'SPRING-y', 'clone_idx', 'fate_observed', 't0_fated', 'train'
    var: 'gene_ids', 'hv_gene', 'must_include', 'exclude', 'use_genes'
    uns: 'fate_counts', 'h5ad_path', 'time_occupance'
    obsm: 'X_clone', 'X_pca', 'X_umap', 'cell_fate_df'
    layers: 'X_scaled'

[3]:

F_obs = larry.tasks.fate_prediction.F_obs

[9]:

def negative_cross_entropy(df1, df2):
    # Ensure that the dataframes have the same shape
    assert df1.shape == df2.shape, "DataFrames must have the same shape"

    df1 = df1.sort_index(axis=1)
    df2 = df2.sort_index(axis=1)

    # Convert the dataframes to numpy arrays for easier manipulation
    arr1 = df1.values
    arr2 = df2.values

    # Clip values to avoid log(0), which is undefined
    epsilon = 1e-12
    arr1 = np.clip(arr1, epsilon, 1.0 - epsilon)
    arr2 = np.clip(arr2, epsilon, 1.0 - epsilon)

    # Calculate negative cross-entropy row by row
    return -np.sum(arr2 * np.log(arr1), axis=1)


def augment(F_obs, F_hat):
    for col in F_obs:
        if not col in F_hat:
            F_hat[col] = 0


def get_sorted_best_predictions(F_hat: pd.DataFrame, N: int = 3):
    F_hat = F_hat.div(F_hat.sum(1), axis=0)
    n_fate_F_obs = F_obs.loc[(F_obs > 0).sum(1) == N]
    n_fate_F_hat = F_hat.loc[n_fate_F_obs.index.astype(int)]
    filt_f_hat = n_fate_F_hat.loc[(n_fate_F_hat > 0).sum(1) == N]
    filt_f_obs = F_obs.loc[filt_f_hat.index.astype(str)]
    filt_nce = negative_cross_entropy(filt_f_obs, filt_f_hat)
    sorted_best = filt_f_hat.iloc[np.argsort(filt_nce)]
    return sorted_best


def plot_lineage(adata_lin: anndata.AnnData, axes):

    coarse_cmap = {2: "#fec729", 4: "#cc4a77", 6: "#2f2d85"}

    axes = cp.umap(
        adata_lin,
        groupby="Time point",
        ax=axes[0],
        force_zorder={2: 301, 4: 302, 6: 303},
        c="k",
        s=80,
    )
    axes = cp.umap(
        adata_lin,
        groupby="Time point",
        cmap=coarse_cmap,
        ax=axes[0],
        force_zorder={2: 311, 4: 312, 6: 313},
        s=40,
    )


def plot(adata_ref, adata_sim, cell_idx, version, img_path):

    axes = cp.umap_manifold(
        adata_ref,
        groupby="Cell type annotation",
        c_background=larry.pl.InVitroColorMap()._dict,
    )

    adata_sim.obsm["X_umap"] = umap_model.transform(adata_sim.X)
    xu = adata_sim.obsm["X_umap"]

    c = adata_sim.obs["t"]
    c_idx = np.argsort(c)
    axes[0].scatter(
        xu[c_idx, 0],
        xu[c_idx, 1],
        c=c[c_idx],
        s=25,
        zorder=201,
        cmap=sdq_an.pl.temporal_colormap,
        rasterized=True,
        alpha=0.5,
        ec="None",
    )

    clone_idx = adata_ref.obs.loc[str(cell_idx)]["clone_idx"]
    adata_lin = adata_ref[adata_ref.obs["clone_idx"] == clone_idx]
    plot_lineage(adata_lin, axes=axes)
    xu_init = adata_sim[adata_sim.obs["t"] == 2].obsm["X_umap"].mean(0)
    axes[0].scatter(
        xu_init[0],
        xu_init[1],
        c="k",
        s=80,
        zorder=450,
        ec="None",
    )
    axes[0].scatter(
        xu_init[0],
        xu_init[1],
        c="dodgerblue",
        s=40,
        zorder=451,
        ec="None",
    )
    axes[0].set_title(cell_idx, fontsize=10)
    plt.savefig(
        img_path,
        dpi=500,
    )
    plt.show()


def plot_n_best(F_hat, n_fates: int = 1, version: int = 0, N: int = 10):
    #     path = getattr(best_ckpts["ckpt_path"], f"version_{version}")
    indices = get_sorted_best_predictions(F_hat, N=n_fates).head(N).index.tolist()
    for cell_idx in indices:
        img_path = f"./scdiffeq_simulation_plots/scdiffeq.simulation.version_{version}.{cell_idx}.{n_fates}_fates.svg"
        if not os.path.exists(img_path):
            adata_sim = sdq.io.read_h5ad(f"./version_{version}/adata_{cell_idx}.h5ad")
            plot(adata_ref, adata_sim, cell_idx, version, img_path)

[10]:

for path in glob.glob("../LARRY.full_dataset.F_hat.scdiffeq.version_*"):
    v = int(path.split("version_version_")[1].split(".")[0])
    F_hat = pd.read_csv(path, index_col=0).drop("Undifferentiated", axis=1)
    augment(F_obs, F_hat)
    plot_n_best(F_hat, n_fates=1, version=v, N=10)
    plot_n_best(F_hat, n_fates=2, version=v, N=10)
    plot_n_best(F_hat, n_fates=3, version=v, N=10)

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_11.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_13.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_15.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_17.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_19.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_21.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_23.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_25.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_27.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_29.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_31.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_33.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_35.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_37.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_39.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_41.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_43.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_45.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_47.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_49.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_51.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_53.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_55.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_57.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_59.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_61.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_63.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_65.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_67.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_69.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_71.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_73.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_75.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_77.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_79.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_81.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_83.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_85.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_87.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_89.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_91.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_93.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_95.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_97.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_99.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_101.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_103.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_105.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_107.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_109.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_111.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_113.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_115.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_117.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_119.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_121.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_123.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_125.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_127.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_129.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_131.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_133.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_135.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_137.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_139.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_141.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_143.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_145.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_147.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_149.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_151.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_153.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_155.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_157.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_159.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_161.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_163.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_165.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_167.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_169.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_171.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_173.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_175.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_177.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_179.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_181.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_183.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_185.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_187.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_189.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_191.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_193.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_195.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_197.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_199.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_201.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_203.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_205.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_207.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_209.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_211.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_213.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_215.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_217.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_219.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_221.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_223.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_225.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_227.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_229.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_231.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_233.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_235.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_237.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_239.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_241.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_243.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_245.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_247.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_249.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_251.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_253.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_255.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_257.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_259.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_261.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_263.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_265.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_267.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_269.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_271.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_273.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_275.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_277.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_279.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_281.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_283.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_285.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_287.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_289.png

AnnData object with n_obs × n_vars = 82000 × 50
    obs: 't', 'z0_idx', 'sim_i', 'sim', 'state', 'fate', 'drift', 'diffusion'
    uns: 'fate_counts', 'h5ad_path', 'sim_idx', 'simulated'
    obsm: 'X_diffusion', 'X_drift'

../_images/_analyses_Figure4ABC_5_291.png

[1]:

import scdiffeq_analyses as sdq_an

[2]:

sdq_an.pl.temporal_colormap

[2]:

TemporalColorMap

under

bad

over

[ ]: