update tutorials.

STOmics · Mar 29, 2024 · 1107d49 · 1107d49
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diff --git a/docs/source/Tutorials/Cell_Correction.ipynb b/docs/source/Tutorials/Cell_Correction.ipynb
@@ -22,28 +22,6 @@
     "    correcting from GEM and mask."
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "055c2cb0",
-   "metadata": {},
-   "source": [
-    "<div class=\"alert alert-info\">\n",
-    "\n",
-    "**Preparation**\n",
-    "\n",
-    "Before **Cell Segmentation**, **Tissue Segmentation** or generating **mask file** from **ssDNA image** on **Cell Correction**, certain packages should be installed beforehand.  \n",
-    "\n",
-    "Install necessary packages by running commands as below:\n",
-    "\n",
-    "> &ensp;&ensp; **pip install tensorflow==2.7.0**  \n",
-    "> &ensp;&ensp; **pip install torch==1.10.0**  \n",
-    "> &ensp;&ensp; **pip install torchvision==0.11.1**  \n",
-    "> &ensp;&ensp; **pip install albumentations==0.4.6**\n",
-    "\n",
-    "</div>"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",

diff --git a/docs/source/Tutorials/Clustering_by_GPU.ipynb b/docs/source/Tutorials/Clustering_by_GPU.ipynb
@@ -77,17 +77,9 @@
    "id": "6c54f9b2",
    "metadata": {},
    "source": [
-    "Select the correct version on the homepage of [RAPIDS' official website](https://rapids.ai/start.html). Run following command to build up a specific environment:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6af3dcbf",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "conda create -n rapids-22.12 -c rapidsai -c conda-forge -c nvidia rapids=22.12 python=3.8 cudatoolkit=11.5"
+    "Select the correct version on the homepage of [RAPIDS' official website](https://rapids.ai/start.html). Run following command to build up a specific environment:\n",
+    "\n",
+    "    conda create -y -n stereopy-rapids -c rapidsai -c conda-forge -c nvidia python=3.8 rapids=23.04.01 cuda-version=11.8"
    ]
   },
   {
@@ -120,17 +112,13 @@
    "id": "4d7987c1",
    "metadata": {},
    "source": [
-    "Installation through conda command fails in the environment with GPU acceleration, only [PyPI command](https://stereopy.readthedocs.io/en/latest/General/Installation.html#pypi) will succeed."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ff9da4be",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pip install stereopy"
+    "Installation through conda command fails in the environment with GPU acceleration, only [PyPI command](https://stereopy.readthedocs.io/en/latest/General/Installation.html#pypi) will succeed.\n",
+    "\n",
+    "    pip install stereopy\n",
+    "\n",
+    "After installing stereopy, you will get some warnings about dependency conflicts, you can ignore them except two that must be reinstall to correct version.\n",
+    "\n",
+    "    pip install dask==2023.3.2 distributed==2023.3.2.1"
    ]
   },
   {

diff --git a/docs/source/Tutorials/SingleR.ipynb b/docs/source/Tutorials/SingleR.ipynb
diff --git a/docs/source/Tutorials/Tissue_Segmentation.ipynb b/docs/source/Tutorials/Tissue_Segmentation.ipynb
diff --git a/docs/source/Tutorials/Trajectory_Analysis.ipynb b/docs/source/Tutorials/Trajectory_Analysis.ipynb
diff --git a/docs/source/content/035_API_Tools.rst b/docs/source/content/035_API_Tools.rst
@@ -16,3 +16,4 @@ The module helps correct cell segmentation and generates corresponding CGEF file
 
     tools.cell_correct.cell_correct
     tools.cell_cut.CellCut.cell_cut
+    tools.tissue_extraction.tissue_extraction_to_bgef
diff --git a/docs/source/content/06_Release_notes.rst b/docs/source/content/06_Release_notes.rst
@@ -3,6 +3,26 @@ Release Notes
 
 .. role:: small
 
+Version 1.2.0
+------------------
+1.2.0 : 2024-03-30
+~~~~~~~~~~~~~~~~~~~
+
+Features:
+
+1. `st.io.read_gem` and `st.io.read_gef` support expression matrix files with geneID information.
+2. Analysis results of `find_marker_genes`  will be saved into the output AnnData h5ad.
+3. Upgraded tissue segmentation algorithm.
+4. Addition of `st.tl.adjusted_rand_score` to calculate the adjusted Rand coefficient between two clusters.
+5. Addition of `st.tl.silhouette_score` to calculate the average silhouette coefficient of a cluster.
+6. `h5ad2rds.R` is compatible with AnnData version > 0.7.5, to convert from h5ad to rds files.
+7. Addition of the clustering category labels to the graph of `st.plt.paga_compare`.
+
+BUG Fixes:
+
+1. Fixed the error of high memory consumption when converting `X.raw` into AnnData.
+
+
 Version 1.1.0
 ------------------
 1.1.0 : 2024-01-17

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -71,6 +71,24 @@ Workflow
 Latest Additions
 ------------------
 
+Version 1.2.0
+~~~~~~~~~~~~~~~~~~~
+1.2.0 : 2024-03-30
+
+Features:
+
+1. `st.io.read_gem` and `st.io.read_gef` support expression matrix files with geneID information.
+2. Analysis results of `find_marker_genes`  will be saved into the output AnnData h5ad.
+3. Upgraded tissue segmentation algorithm.
+4. Addition of `st.tl.adjusted_rand_score` to calculate the adjusted Rand coefficient between two clusters.
+5. Addition of `st.tl.silhouette_score` to calculate the average silhouette coefficient of a cluster.
+6. `h5ad2rds.R` is compatible with AnnData version > 0.7.5, to convert from h5ad to rds files.
+7. Addition of the clustering category labels to the graph of `st.plt.paga_compare`.
+
+BUG Fixes:
+
+1. Fixed the error of high memory consumption when converting `X.raw` into AnnData.
+
 Version 1.1.0
 ~~~~~~~~~~~~~~
 1.1.0 : 2024-01-17
@@ -116,37 +134,6 @@ BUG Fixes:
 7. There is NaN in Cell Community Detection output after threshold filtering, resulting in a calculating error when performed Find marker genes based on it.
 8. `st.plt.paga_time_series_plot` indicated the image is too large to draw, leading to graph overlap, due to the limitation of matplotlib package.
 
-Version 0.14.0b1 (Beta)
-~~~~~~~~~~~~~~~~~~~~~~~~~
-0.14.0b1 : 2023-9-15
-
-Notice: this Beta version is specifically developed for multi-sample analysis.
-
-Features:
-
-1. Addition of Cell Community Detection (CCD) analysis.
-2. Addition of Cell Co-occurrence analysis.
-3. Addition of Cellpose in cell segmentation, especially for cell cytoplasm using `model_type='cyto2'`.
-4. Addition of circos (`st.plt.ccc_circos_plot`) and sankey (`st.plt.ccc_sankey_plot`) plots in Cell-cell Communication analysis.
-5. Addition of volcano (`st.plt.TVG_volcano_plot`) and tree (`st.plt.time_series_tree_plot`) plots in Time Series analysis.
-6. Addition of PAGA tree plot, `st.plt.paga_plot`.
-7. Addition of visuallization of `st.tl.dendrogram`.
-8. Addition of version check using `st.__version__`.
-9. Supported obtain subset from a data object, using clustering output, by `st.tl.filter_by_clusters`.
-10. Supported filtering data using hvgs, by `st.tl.filter_by_hvgs`.
-11. Supported mapping the clustering result of SquareBin analysis to the same data but in CellBin.
-12. Supported writing annotation information into CGEF file, only clustering result available before.
-13. Supported saving images of PNG and PDF formats, in interactive interface.
-14. Optimized the function of `st.tl.find_marker_genes`.
-15. Optimized the modification of titles in horizontal axis, vertical axis and plot.
-
-BUG Fixes:
-
-1. Fixed the issue that SingleR calculating did not add filtration to the column field when traversing expression matrix, resulting in the subsequent absence of the column index.
-2. Fixed the issue that output Seurat h5ad could not be transformed into R format.
-3. Fixed the issue that clustering output of Leiden was in wrong data type under the scene of GPU acceleration, leading to errors in subsequent analysis which work on the clustering result.
-4. Fixed the issue that clustering result could not be written into GEF file, using `st.io.update_gef`, caused by data type error. From v0.12.1 on, `date.cells.cell_name` has changed from int to string. 
-
 
 .. toctree::
     :titlesonly:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -16,3 +16,4 @@ The module helps correct cell segmentation and generates corresponding CGEF file

		tools.cell_correct.cell_correct
		tools.cell_cut.CellCut.cell_cut
		tools.tissue_extraction.tissue_extraction_to_bgef