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fix key in mtp.cell_transition #61

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Feb 2, 2024
Merged

fix key in mtp.cell_transition #61

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0edb869
fix key in mtp.cell_transition
Feb 2, 2024
c514780
outdated arguments sankey
Feb 2, 2024
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10 changes: 4 additions & 6 deletions examples/plotting/300_sankey.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@
"source": [
"As with all plotting functionalities in {mod}`moscot`, we first call the {meth}`~moscot.problems.time.TemporalProblem.sankey` method of the problem class, which stores the results of the computation in the {class}`~anndata.AnnData` instance. Let us assume we want to plot the Sankey diagram across all time points 2, 3, 4, and 7 . Moreover, we want the Sankey diagram to visualize flows between cell types. In general, we can visualize the flow defined by any categorical column in {attr}`~anndata.AnnData.obs` via the `source_groups` and the `target_groups` parameters, respectively.\n",
"\n",
"In this example, we are interested in descendants as opposed to ancestors, which is why we choose `forward = True`. The information required to plot the Sankey diagram is provided in transition matrices, which we would obtain by `return_data = True`. Here, we are only interested in the visualization."
"In this example, we are interested in descendants as opposed to ancestors, which is why we choose `forward = True`. The information required to plot the Sankey diagram is provided in transition matrices, which are saved to {attr}`~anndata.AnnData.uns['moscot_results']['sankey']` by default. Here, we are only interested in the visualization."
]
},
{
Expand All @@ -134,7 +134,6 @@
" source_groups=\"cell_type\",\n",
" target_groups=\"cell_type\",\n",
" forward=True,\n",
" return_data=False,\n",
")"
]
},
Expand Down Expand Up @@ -206,10 +205,9 @@
" source_groups={\"cell_type\": [\"HSC\", \"MasP\", \"MkP\"]},\n",
" target_groups={\"cell_type\": [\"HSC\", \"MasP\", \"MkP\"]},\n",
" forward=True,\n",
" return_data=False,\n",
" key_added=new_key,\n",
")\n",
"mtp.sankey(tp, dpi=100, title=\"Cell type evolution over time\", uns_key=new_key)"
"mtp.sankey(tp, dpi=100, title=\"Cell type evolution over time\", key=new_key)"
]
}
],
Expand All @@ -223,7 +221,7 @@
"kernelspec": {
"display_name": "moscot",
"language": "python",
"name": "moscot"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -235,7 +233,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.9"
"version": "3.11.5"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions tutorials/200_temporal_problem.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -581,7 +581,7 @@
" figsize=(5, 5),\n",
" return_fig=True,\n",
" ax=axes[0],\n",
" uns_key=\"transitions_2_3\",\n",
" key=\"transitions_2_3\",\n",
")\n",
"\n",
"axes[1] = mtp.cell_transition(\n",
Expand All @@ -590,7 +590,7 @@
" figsize=(5, 5),\n",
" return_fig=True,\n",
" ax=axes[1],\n",
" uns_key=\"transitions_3_4\",\n",
" key=\"transitions_3_4\",\n",
")\n",
"\n",
"axes[2] = mtp.cell_transition(\n",
Expand All @@ -599,7 +599,7 @@
" figsize=(5, 5),\n",
" return_fig=True,\n",
" ax=axes[2],\n",
" uns_key=\"transitions_4_7\",\n",
" key=\"transitions_4_7\",\n",
")\n",
"\n",
"fig.subplots_adjust(wspace=0.4)"
Expand Down Expand Up @@ -866,7 +866,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.10"
"version": "3.11.5"
},
"vscode": {
"interpreter": {
Expand Down
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