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theislab · Oct 5, 2023 · aefddec · aefddec
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Showing 6 changed files with 52 additions and 43 deletions.
diff --git a/jupyter-book/surface_protein/annotation.ipynb b/jupyter-book/surface_protein/annotation.ipynb
@@ -74,7 +74,7 @@
    "source": [
     "adata = sc.read(\n",
     "    \"cite_preprocessed.h5ad\",\n",
-    "    backup_url='https://figshare.com/ndownloader/files/42569866'\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/42569866\",\n",
     ")"
    ]
   },

diff --git a/jupyter-book/surface_protein/batch_correction.ipynb b/jupyter-book/surface_protein/batch_correction.ipynb
@@ -76,8 +76,10 @@
    "source": [
     "cite_xdbt = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452434\",\n",
-    "    fname='cite_doublet_removal_xdbt.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_doublet_removal_xdbt.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -88,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata = mu.read('cite_doublet_removal_xdbt.h5mu')"
+    "mdata = mu.read(\"cite_doublet_removal_xdbt.h5mu\")"
    ]
   },
   {
@@ -390,7 +392,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata.write('cite_batch_correction.h5mu')"
+    "mdata.write(\"cite_batch_correction.h5mu\")"
    ]
   },
   {

diff --git a/jupyter-book/surface_protein/dimensionality_reduction.ipynb b/jupyter-book/surface_protein/dimensionality_reduction.ipynb
@@ -80,8 +80,10 @@
    "source": [
     "cite_xdbt = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452434\",\n",
-    "    fname='cite_doublet_removal_xdbt.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_doublet_removal_xdbt.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -102,7 +104,7 @@
    },
    "outputs": [],
    "source": [
-    "mdata = mu.read('cite_doublet_removal_xdbt.h5mu')"
+    "mdata = mu.read(\"cite_doublet_removal_xdbt.h5mu\")"
    ]
   },
   {
@@ -178,11 +180,7 @@
     }
    ],
    "source": [
-    "temp = (\n",
-    "    mdata[\"prot\"]\n",
-    "    .var.loc[~mdata[\"prot\"].var.index.isin(isotype_controls), :]\n",
-    "    .index\n",
-    ")\n",
+    "temp = mdata[\"prot\"].var.loc[~mdata[\"prot\"].var.index.isin(isotype_controls), :].index\n",
     "temp"
    ]
   },
@@ -467,7 +465,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata.write('cite_dimensionality_reduction.h5mu')"
+    "mdata.write(\"cite_dimensionality_reduction.h5mu\")"
    ]
   },
   {

diff --git a/jupyter-book/surface_protein/doublet_detection.ipynb b/jupyter-book/surface_protein/doublet_detection.ipynb
@@ -70,8 +70,10 @@
    "source": [
     "cite_filtered = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452443\",\n",
-    "    fname='cite_normalization.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_normalization.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -82,7 +84,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata = mu.read('cite_normalization.h5mu')"
+    "mdata = mu.read(\"cite_normalization.h5mu\")"
    ]
   },
   {
@@ -378,7 +380,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata.write('cite_doublet_removal_xdbt.h5mu')"
+    "mdata.write(\"cite_doublet_removal_xdbt.h5mu\")"
    ]
   },
   {

diff --git a/jupyter-book/surface_protein/normalization.ipynb b/jupyter-book/surface_protein/normalization.ipynb
@@ -52,7 +52,8 @@
     "import scanpy as sc\n",
     "\n",
     "import warnings\n",
-    "warnings.filterwarnings('ignore')\n",
+    "\n",
+    "warnings.filterwarnings(\"ignore\")\n",
     "\n",
     "sc.settings.verbosity = 0\n",
     "sc.settings.set_figure_params(\n",
@@ -79,8 +80,10 @@
    "source": [
     "cite_quality_control = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452449\",\n",
-    "    fname='cite_quality_control.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_quality_control.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -131,7 +134,7 @@
     }
    ],
    "source": [
-    "mdata = mu.read('cite_quality_control.h5mu')\n",
+    "mdata = mu.read(\"cite_quality_control.h5mu\")\n",
     "mdata"
    ]
   },
@@ -172,7 +175,7 @@
     }
    ],
    "source": [
-    "mdata_raw = mu.read('cite_raw.h5mu')\n",
+    "mdata_raw = mu.read(\"cite_raw.h5mu\")\n",
     "mdata_raw"
    ]
   },
@@ -394,7 +397,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata.write('cite_normalization.h5mu')"
+    "mdata.write(\"cite_normalization.h5mu\")"
    ]
   },
   {

diff --git a/jupyter-book/surface_protein/quality_control.ipynb b/jupyter-book/surface_protein/quality_control.ipynb
@@ -103,12 +103,12 @@
    "source": [
     "# ToDo adjust this\n",
     "rna = sc.read_10x_h5(\n",
-    "    filename=\"rna_filtered_feature_bc_matrix.h5\", \n",
-    "    backup_url='https://figshare.com/ndownloader/files/39546196'\n",
+    "    filename=\"rna_filtered_feature_bc_matrix.h5\",\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/39546196\",\n",
     ")\n",
     "prot = sc.read_10x_h5(\n",
-    "    filename=\"prot_filtered_feature_bc_matrix.h5\", \n",
-    "    backup_url='https://figshare.com/ndownloader/files/42569008'\n",
+    "    filename=\"prot_filtered_feature_bc_matrix.h5\",\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/42569008\",\n",
     ")"
    ]
   },
@@ -198,12 +198,12 @@
    "source": [
     "# ToDo adjust this\n",
     "rna_raw = sc.read_10x_h5(\n",
-    "    filename=\"rna_raw_feature_bc_matrix.h5\", \n",
-    "    backup_url='https://figshare.com/ndownloader/files/39546217'\n",
+    "    filename=\"rna_raw_feature_bc_matrix.h5\",\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/39546217\",\n",
     ")\n",
     "prot_raw = sc.read_10x_h5(\n",
-    "    filename=\"prot_raw_feature_bc_matrix.h5\", \n",
-    "    backup_url='https://figshare.com/ndownloader/files/42569026'\n",
+    "    filename=\"prot_raw_feature_bc_matrix.h5\",\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/42569026\",\n",
     ")\n",
     "mdata_raw = mu.MuData({\"rna\": rna_raw, \"prot\": prot_raw})\n",
     "mdata_raw"
@@ -228,8 +228,10 @@
    "source": [
     "cite_filtered = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452287\",\n",
-    "    fname='cite_filtered.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_filtered.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -242,8 +244,10 @@
    "source": [
     "cite_raw = pooch.retrieve(\n",
     "    url=\"https://figshare.com/ndownloader/files/41452308\",\n",
-    "    fname='cite_raw.h5mu', path='.',\n",
-    "    known_hash=None, progressbar=True, \n",
+    "    fname=\"cite_raw.h5mu\",\n",
+    "    path=\".\",\n",
+    "    known_hash=None,\n",
+    "    progressbar=True,\n",
     ")"
    ]
   },
@@ -284,7 +288,7 @@
     }
    ],
    "source": [
-    "mdata = md.read_h5mu('cite_filtered.h5mu')\n",
+    "mdata = md.read_h5mu(\"cite_filtered.h5mu\")\n",
     "mdata"
    ]
   },
@@ -325,7 +329,7 @@
     }
    ],
    "source": [
-    "mdata_raw = md.read_h5mu('cite_raw.h5mu')\n",
+    "mdata_raw = md.read_h5mu(\"cite_raw.h5mu\")\n",
     "mdata_raw"
    ]
   },
@@ -570,9 +574,7 @@
    ],
    "source": [
     "sns.displot(\n",
-    "    mdata[\"prot\"]\n",
-    "    .obs.query(\"total_counts>20000 and total_counts<100000\")\n",
-    "    .total_counts\n",
+    "    mdata[\"prot\"].obs.query(\"total_counts>20000 and total_counts<100000\").total_counts\n",
     ")"
    ]
   },
@@ -620,7 +622,9 @@
    ],
    "source": [
     "sns.displot(\n",
-    "    mdata_raw[\"rna\"].obs.sample(frac=0.01).query(\"total_counts<100000 and total_counts>10\"),\n",
+    "    mdata_raw[\"rna\"]\n",
+    "    .obs.sample(frac=0.01)\n",
+    "    .query(\"total_counts<100000 and total_counts>10\"),\n",
     "    x=\"total_counts\",\n",
     "    log_scale=True,\n",
     "    hue=\"donor\",\n",
@@ -1139,7 +1143,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdata.write('cite_quality_control.h5mu')"
+    "mdata.write(\"cite_quality_control.h5mu\")"
    ]
   },
   {