📝 add annotation nb

docs/examples/01_preprocess_cytof_Oetjen.ipynb

@@ -5,7 +5,7 @@
    "id": "0b85a563",
    "metadata": {},
    "source": [
-    "# Human bone marrow of healthy human donors \n",
+    "# Human bone marrow of healthy human donors - Preprocessing\n",
     "\n",
     "In this notebook, we pre-process cyTOF data of bone marrow samples from 8 healthy donors. Data were provided by Oetjen et al (JCl Insight, 2018). \n",
     "We employ the following steps:\n",

docs/examples/index.md

@@ -7,7 +7,6 @@ The notebooks do **not** get executed in CI for testing because they involve lar
 ```{toctree}
 :maxdepth: 1
 :glob:
-:reversed:
 
 *
 ```

docs/tutorials/read_fcs.ipynb

@@ -58,6 +58,13 @@
     "adata"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The `.var` section of the AnnData object contains the channel information. We set the marker names as `var_names` by default. In addition, we save the channel information in the `\"channel\"` column. "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -71,7 +78,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `.var` section of the AnnData object contains the channel information. We set the marker names as `var_names` by default. In addition, we save the channel information in the `\"channel\"` column. "
+    "The `.uns['meta']` section contains the header information from the FCS file."
    ]
   },
   {
@@ -80,14 +87,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata.var"
+    "adata.uns[\"meta\"]"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `.uns['meta']` section contains the header information from the FCS file."
+    "## Missing marker column\n",
+    "\n",
+    "In some FCS files, the marker information does not follow the `$P[0-9]S` pattern, and reading the FCS file might fail. You can set the `reindex=False` option when reading the FCS files."
    ]
   },
   {
@@ -96,13 +105,38 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata.uns[\"meta\"]"
+    "adata = pm.io.read_fcs(path_data, reindex=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The `.var` section of the AnnData object contains the channel information. Here we use a running number as `var_names`. The marker names may be created manually from the `channel` column. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata.var"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('py39')",
+   "display_name": "Python 3.9.7 ('pyto_dev')",
    "language": "python",
    "name": "python3"
   },
@@ -116,11 +150,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.7"
   },
   "vscode": {
    "interpreter": {
-    "hash": "ae1fefc8646a06dd2e75004cd934adda7c5727b046986a772e3b44b0ffba9754"
+    "hash": "48c3c4927e81daf79217bae0bb1c93e3ab00a11990990ff2e155253980f357b0"
    }
   }
  },

pytometry/__init__.py

@@ -20,7 +20,7 @@
 
 """
 
-__version__ = "0.1.2"  # denote a pre-release for 0.1.0 with 0.1a1
+__version__ = "0.1.3"  # denote a pre-release for 0.1.0 with 0.1a1
 
 from . import plotting as pl
 from . import preprocessing as pp