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Added tasccoda example plots #527

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Feb 9, 2024
Merged

Added tasccoda example plots #527

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98e2920
tasccoda plots
namsaraeva Feb 6, 2024
81b9ed5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 6, 2024
a0b2408
add tasccoda umap and small fixes
namsaraeva Feb 8, 2024
1f9b4d7
Merge branch 'main' into tasccoda_plots
namsaraeva Feb 8, 2024
2bf8668
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 8, 2024
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Binary file added docs/_static/docstring_previews/tasccoda_draw_effects.png
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16 changes: 0 additions & 16 deletions pertpy/plot/_coda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,9 +112,6 @@ def stacked_barplot( # pragma: no cover
>>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
sample_identifier="batch", covariate_obs=["condition"])
>>> sccoda.plot_stacked_barplot(mdata, feature_name="samples")

Preview:
.. image:: ../_static/docstring_previews/sccoda_stacked_barplot.png
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down Expand Up @@ -188,9 +185,6 @@ def effects_barplot( # pragma: no cover
>>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
>>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
>>> sccoda.plot_effects_barplot(mdata)

Preview:
.. image:: ../_static/docstring_previews/sccoda_effects_barplot.png
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down Expand Up @@ -268,9 +262,6 @@ def boxplots( # pragma: no cover
>>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
sample_identifier="batch", covariate_obs=["condition"])
>>> sccoda.plot_boxplots(mdata, feature_name="condition", add_dots=True)

Preview:
.. image:: ../_static/docstring_previews/sccoda_boxplots.png
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down Expand Up @@ -341,9 +332,6 @@ def rel_abundance_dispersion_plot( # pragma: no cover
>>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
>>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
>>> sccoda.plot_rel_abundance_dispersion_plot(mdata)

Preview:
.. image:: ../_static/docstring_previews/sccoda_rel_abundance_dispersion_plot.png
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down Expand Up @@ -512,8 +500,6 @@ def draw_effects( # pragma: no cover
>>> )
>>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
>>> tasccoda.plot_draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage")

Preview: #TODO: Add preview
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down Expand Up @@ -603,8 +589,6 @@ def effects_umap( # pragma: no cover
>>> "effect_df_condition[T.Hpoly.Day10]"],
>>> cluster_key="nsbm_level_1",
>>> )

Preview: #TODO: Add preview
"""
warnings.warn(
"This function is deprecated and will be removed in pertpy 0.8.0!"
Expand Down
21 changes: 18 additions & 3 deletions pertpy/tools/_coda/_base_coda.py
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Expand Up @@ -1864,6 +1864,9 @@ def plot_draw_tree( # pragma: no cover
>>> )
>>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
>>> tasccoda.plot_draw_tree(mdata, tree="lineage")

Preview:
.. image:: /_static/docstring_previews/tasccoda_draw_tree.png
"""
try:
from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces
Expand Down Expand Up @@ -1954,7 +1957,10 @@ def plot_draw_effects( # pragma: no cover
>>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
>>> )
>>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
>>> pt.pl.coda.draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage")
>>> tasccoda.plot_draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage")

Preview:
.. image:: /_static/docstring_previews/tasccoda_draw_effects.png
"""
try:
from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces
Expand Down Expand Up @@ -2124,15 +2130,17 @@ def plot_effects_umap( # pragma: no cover
Examples:
Example with tascCODA:
>>> import pertpy as pt
>>> import scanpy as sc
>>> import schist
>>> adata = pt.dt.haber_2017_regions()
>>> schist.inference.nested_model(adata, samples=100, random_seed=5678)
>>> sc.pp.neighbors(adata)
>>> schist.inference.nested_model(adata, n_init=100, random_seed=5678)
>>> tasccoda_model = pt.tl.Tasccoda()
>>> tasccoda_data = tasccoda_model.load(adata, type="cell_level",
>>> cell_type_identifier="nsbm_level_1",
>>> sample_identifier="batch", covariate_obs=["condition"],
>>> levels_orig=["nsbm_level_4", "nsbm_level_3", "nsbm_level_2", "nsbm_level_1"],
>>> add_level_name=True)sccoda = pt.tl.Sccoda()
>>> add_level_name=True)
>>> tasccoda_model.prepare(
>>> tasccoda_data,
>>> modality_key="coda",
Expand All @@ -2144,12 +2152,19 @@ def plot_effects_umap( # pragma: no cover
>>> tasccoda_model.run_nuts(
... tasccoda_data, modality_key="coda", rng_key=1234, num_samples=10000, num_warmup=1000
... )
>>> tasccoda_model.run_nuts(
... tasccoda_data, modality_key="coda", rng_key=1234, num_samples=10000, num_warmup=1000
... )
>>> sc.tl.umap(tasccoda_data["rna"])
>>> tasccoda_model.plot_effects_umap(tasccoda_data,
>>> effect_name=["effect_df_condition[T.Salmonella]",
>>> "effect_df_condition[T.Hpoly.Day3]",
>>> "effect_df_condition[T.Hpoly.Day10]"],
>>> cluster_key="nsbm_level_1",
>>> )

Preview:
.. image:: /_static/docstring_previews/tasccoda_effects_umap.png
"""
# TODO: Add effect_name parameter and cluster_key and test the example
data_rna = data[modality_key_1]
Expand Down
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