diff --git a/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb b/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb index 90a28d0..f043ed1 100644 --- a/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb +++ b/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb @@ -190,7 +190,7 @@ "\n", "\n", "input_data=sdata.points['transcripts'][['missegmentation_associated']].compute()\n", - "troutpy.pl.pie_of_positive(input_data,groupby='missegmentation_associated',figures_path=output_path,save=True)" + "troutpy.pl.pie_of_positive(input_data,groupby='missegmentation_associated',save=True)" ] } ], diff --git a/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb b/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb index 892a7b2..599475c 100644 --- a/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb +++ b/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb @@ -267,23 +267,21 @@ "outputs": [], "source": [ "def communicating_genes_per_celltype(sdata,proportion_threshold: float = 0.2,cell_type_key='cell type'):\n", - " \"\"\"\n", - " Computes the number of significant genes exchanged between source and target cell types\n", - " based on their proportions in the dataset.\n", + " \"\"\"Computes the number of significant genes exchanged between source and target cell types based on their proportions in the dataset.\n", "\n", " Parameters:\n", " - sdata: AnnData object\n", - " A spatial data object containing the 'table' and 'xrna_metadata' components.\n", + " A spatial data object containing the 'table' and 'xrna_metadata' components.\n", " - proportion_threshold: float, optional (default=0.2)\n", - " The threshold for filtering significant gene proportions. Genes with proportions \n", - " above this value are considered significant.\n", + " The threshold for filtering significant gene proportions. Genes with proportions \n", + " above this value are considered significant.\n", " - cell_type_key: str, optional (default='cell type')\n", - " The key in `adata.obs` that contains the cell type annotations.\n", + " The key in `adata.obs` that contains the cell type annotations.\n", "\n", " Returns:\n", " - number_interactions_df: pandas.DataFrame\n", - " A DataFrame where rows represent source cell types, columns represent target cell \n", - " types, and values indicate the number of significant genes shared between them.\n", + " A DataFrame where rows represent source cell types, columns represent target cell \n", + " types, and values indicate the number of significant genes shared between them.\n", " \"\"\"\n", " adata=sdata['table']\n", " source_proportions=pd.DataFrame(sdata['xrna_metadata'].varm['source'],index=sdata['xrna_metadata'].var.index,columns=adata.obs[cell_type_key].unique().dropna())\n", diff --git a/notebooks/spatialdata_tutorials/7_image_params.ipynb b/notebooks/spatialdata_tutorials/7_image_params.ipynb index fa72e25..347c08f 100644 --- a/notebooks/spatialdata_tutorials/7_image_params.ipynb +++ b/notebooks/spatialdata_tutorials/7_image_params.ipynb @@ -255,30 +255,6 @@ "# The transcripts DataFrame now has a column for each channel's intensity\n" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['DAPI',\n", - " 'ATP1A1/CD45/E-Cadherin',\n", - " '18S',\n", - " 'AlphaSMA/Vimentin',\n", - " 'dummy',\n", - " 'feature_name',\n", - " 'feature_name']" - ] - }, - "execution_count": 75, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [] - }, { "cell_type": "code", "execution_count": null,