update tutorials.

STOmics · Jun 28, 2024 · 66d9537 · 66d9537
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diff --git a/docs/source/Tutorials(Multi-sample)/3D_Cell_Cell_Communication.ipynb b/docs/source/Tutorials(Multi-sample)/3D_Cell_Cell_Communication.ipynb
@@ -493,8 +493,8 @@
    ],
    "source": [
     "ms_data.tl.filter_cells(\n",
-    "        min_gene=1, \n",
-    "        min_n_genes_by_counts=3, \n",
+    "        min_counts=1, \n",
+    "        min_genes=3, \n",
     "        pct_counts_mt=5, \n",
     "        inplace=True\n",
     "        )\n",

diff --git a/docs/source/Tutorials/SingleR.ipynb b/docs/source/Tutorials/SingleR.ipynb
@@ -284,7 +284,7 @@
    "id": "230d105b",
    "metadata": {},
    "source": [
-    "`ref_use_col='ClusterName'` is just an example, the actual value is determined based on the reference you use."
+    "`ref_use_col='ClusterName'` specifies an obs column used for annotating, here is just an example, the actual value depends on the reference to be used."
    ]
   },
   {

diff --git a/docs/source/content/06_Release_notes.rst b/docs/source/content/06_Release_notes.rst
@@ -3,6 +3,24 @@ Release Notes
 
 .. role:: small
 
+Version 1.3.1
+------------------
+1.3.1 : 2024-06-28
+~~~~~~~~~~~~~~~~~~~
+
+Features:
+
+1. Addition of new method **'adaptive'** for `st.tl.get_niche <stereo.algorithm.get_niche.GetNiche.main.html>`_ (the original method is named **'fixed'**).
+2. Changed some parameter names of `st.tl.filter_cells <stereo.core.StPipeline.filter_cells.html>`_ and `st.tl.filter_genes <stereo.core.StPipeline.filter_genes.html>`_ for eliminating ambiguity(old parameter names are still compatible).
+3. Filter the results of **PCA** and **UMAP** simultaneously when running `st.tl.filter_cells`.
+
+BUG Fixes:
+
+1. Fixed the problem that `ms_data.to_isolated` is incompatible with that there are duplicate **cell names** in different samples.
+2. Fixed the problem that `st.io.read_gef` is incompatible with those **GEF** files that contain **gene names** ending with **'_{number}'** (like **'ABC_123'**).
+3. Upgraded **gefpy** to latest for fixing the error that **gene names** are lost after running **CellCorrection**.
+
+
 Version 1.3.0
 ------------------
 1.3.0 : 2024-05-31

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -70,6 +70,22 @@ Workflow
 Latest Additions
 ------------------
 
+Version 1.3.1
+~~~~~~~~~~~~~~~~~~~
+1.3.1 : 2024-06-28
+
+Features:
+
+1. Addition of new method **'adaptive'** for `st.tl.get_niche <content/stereo.algorithm.get_niche.GetNiche.main.html>`_ (the original method is named **'fixed'**).
+2. Changed some parameter names of `st.tl.filter_cells <content/stereo.core.StPipeline.filter_cells.html>`_ and `st.tl.filter_genes <content/stereo.core.StPipeline.filter_genes.html>`_ for eliminating ambiguity(old parameter names are still compatible).
+3. Filter the results of **PCA** and **UMAP** simultaneously when running `st.tl.filter_cells`.
+
+BUG Fixes:
+
+1. Fixed the problem that `ms_data.to_isolated` is incompatible with that there are duplicate **cell names** in different samples.
+2. Fixed the problem that `st.io.read_gef` is incompatible with those **GEF** files that contain **gene names** ending with **'_{number}'** (like **'ABC_123'**).
+3. Upgraded **gefpy** to latest for fixing the error that **gene names** are lost after running **CellCorrection**.
+
 Version 1.3.0
 ~~~~~~~~~~~~~~~~~~~
 1.3.0 : 2024-05-31

diff --git a/stereo/utils/pipeline_utils.py b/stereo/utils/pipeline_utils.py
@@ -165,7 +165,8 @@ def cluster_bins_to_cellbins(
 
     :param bins_data: StereoExpData object of bins.
     :param cellbins_data: StereoExpData object of cellbins.
-    :param bins_cluster_res_key: cluster result key in bins' result.
+    :param bins_cluster_res_key: cluster result key in `bins_data.tl.result`, the mapped result will be named as
+                                `{bins_cluster_res_key}_from_bin` and added into `cellbins_data.tl.result`.
 
     :return: The object of StereoExpData assigned to parameter `cellbins_data`.
     """