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Enable 3D quivers, scatters and streamtube in dynamo #260

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Enable 3D quivers, scatters and streamtube in dynamo #260

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2 changes: 1 addition & 1 deletion docs/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ ipykernel>=5.1.0
nbsphinx>=0.8.6
pygments>=2.6.1

numpy>=1.18.1
numpy>=1.20.0
pandas>=0.25.1
scipy>=1.0
scikit-learn>=0.19.1
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17 changes: 10 additions & 7 deletions docs/source/API.rst
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Expand Up @@ -241,21 +241,24 @@ Vector field (vf)
vf.diffusionMatrix


*Vector field graph*

.. autosummary::
:toctree: _autosummary

vf.vfGraph

Prediction (pd)
~~~~~~~~~~~~~~~

.. autosummary::
:toctree: _autosummary


*Vector field lineage fate*

pd.fate
pd.fate_bias


*Vector field state graph*

.. autosummary::
:toctree: _autosummary

pd.state_graph

Plotting (pl)
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15 changes: 7 additions & 8 deletions dynamo/plot/scVectorField.py
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Expand Up @@ -69,9 +69,9 @@ def cell_wise_vectors_3d(
save_kwargs: dict = {},
quiver_3d_kwargs: dict = {
"zorder": 3,
"length": 2,
"linewidth": 5,
"arrow_length_ratio": 5,
"length": 10,
"linewidth": 1,
"arrow_length_ratio": 0.3,
"norm": cm.colors.Normalize(),
"cmap": cm.PRGn,
},
Expand Down Expand Up @@ -292,7 +292,7 @@ def add_axis_label(ax, labels):
elif save_show_or_return == "show":
plt.show()
elif save_show_or_return == "return":
return axes
return axes, (x0, x1, x2, v0, v1, v2)


def grid_vectors_3d():
Expand Down Expand Up @@ -1687,10 +1687,9 @@ def streamplot_2d(ax):
set_arrow_alpha(ax, streamline_alpha)
set_stream_line_alpha(s, streamline_alpha)

if type(axes_list) == list:
for i in range(len(axes_list)):
ax = axes_list[i]
streamplot_2d(ax)
for i in range(len(axes_list)):
ax = axes_list[i]
streamplot_2d(ax)

if save_show_or_return == "save":
s_kwargs = {
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -21,7 +21,7 @@ keywords = 'dynamo scslam-seq scrna-seq velocity rna protein vector-field potent
license = 'BSD'
module = 'dynamo'
requires = [
'numpy>=1.18.1',
'numpy>=1.20.0',
'pandas>=0.25.1',
'scipy>=1.0',
'scikit-learn>=0.19.1',
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