Dominik J. Otto

Hi all! I was confused about the tag too but am happy to clarify. Pseudotime is defined from one specific start cell and approximates the time a cell would need...

Hello @Merlin2333, Thank you for the inquiry. The kernel is computed by the [`palantir.utils.compute_kernel`](https://palantir.readthedocs.io/en/latest/utils.html#palantir.utils.compute_kernel) function. Under the hood this function uses the `anndata.obsm["X_pca"]` representation to compute the kernel, and it...

Hi @yitengfei120011, thanks for reaching out. From the plot, it appears that only a single terminal state was specified. As a result, the fate probability remains constant at 1 for...

Try seaborns [clustermap](https://seaborn.pydata.org/generated/seaborn.clustermap.html), e.g., for the Monocyte branch of the [tutorial notebook](https://palantir.readthedocs.io/en/latest/notebooks/Palantir_sample_notebook.html): ```Python import seaborn as sns mask = ad.varm["gene_trends_Mono"].var(axis=1) > 0.05 g = sns.clustermap( ad.varm["gene_trends_Mono"].loc[mask], cmap="Spectral_r", z_score=0, row_cluster=True, #...

When plotting gene trends, only cells of specific branch are used. This is explained, e.g., in the [tutorial notebook](https://palantir.readthedocs.io/en/latest/notebooks/Palantir_sample_notebook.html#Gene-expression-trends). The scaling you do in your first example, however, scales the...

Hi @ltzyl, Thanks for reporting this, and apologies, the plot definitely doesn’t look right. The arrows are computed and smoothed based on the positions of cells in the `embedding_basis` (default:...

Hi all! I believe the failing CI checks are due to pre-existing anndata CI configuration issues rather than this PR: - Test failures (hatch-test.min, hatch-test.stable, hatch-test.pre): All fail during dependency...

Bumped pytest>=8.2 to pytest>=9.0 in test-min to resolve dependency conflict with hatch-test's pinned pytest~=9.0. Attempting to trigger codecov to refresh its report with actual coverage: @codecov refresh

Oh, thanks so much for the update @Zethson! Totally understand, and no rush at all. This one is a bit larger, and I figured it might take some time. I...

Thank you for the feedback, I really appreciate it! ## Extensibility via Formatters To accommodate new modalities like spatial data, I implemented two extension points: - **`SectionFormatter`** - Define visualization...