update some api comments.

stereo/algorithm/st_gears/main.py

@@ -52,7 +52,7 @@ def main(
         :param start_i: The index of first sample to calulate, defaults to 0
         :param end_i: The index of last sample to calulate, defaults to None.
                         By default, it is the last of all samples.
-        :param tune_alpha_li: List of regularization factor in Fused Gromov Wasserstin (FGW) OT problem formulation, to be
+        :param tune_alpha_li: List of regularization factor in Fused Gromov Wasserstein (FGW) OT problem formulation, to be
                         automatically tunned. Refer to this paper for the FGW formulation:
                         Optimal transport for structured data with application on graphs. T Vayer, L Chapel, R Flamary,
                         R Tavenard… - arXiv preprint arXiv …, 2018 - arxiv.org

stereo/core/st_pipeline.py

@@ -496,7 +496,7 @@ def log1p(
         inplace
             whether to replace the data.exp_matrix or save the result in `data.layers`.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
         res_key
             the key to save the result in `data.layers` when `inplace` is False or `add_layer` is True.
 
@@ -535,7 +535,7 @@ def normalize_total(
         inplace
             whether to replace the data.exp_matrix or save the result in `data.layers`.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
         res_key
             the key to save the result in `data.layers` when `inplace` is False or `add_layer` is True.
 
@@ -576,7 +576,7 @@ def scale(
         inplace
             whether to replace the data.exp_matrix or save the result in `data.layers`.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
         res_key
             the key to save the result in `data.layers` when `inplace` is False or `add_layer` is True.
 
@@ -612,7 +612,7 @@ def quantile(
         inplace
             whether to replace the data.exp_matrix or save the result in `data.layers`.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
         res_key
             the key to save the result in `data.layers` when `inplace` is False or `add_layer` is True.
         
@@ -653,7 +653,7 @@ def disksmooth_zscore(
         inplace
             whether to replace the data.exp_matrix or save the result in `data.layers`.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
         res_key
             the key to save the result in `data.layers` when `inplace` is False or `add_layer` is True.
         
@@ -714,7 +714,7 @@ def sctransform(
         layer
             the key of layer to be used instead of the data.exp_matrix.
         add_layer
-            whether to save the result in `data.layers` simultaneously when `inplace` is False.
+            whether to save the result in `data.layers` simultaneously when `inplace` is True.
 
         Returns
         -----------

stereo/io/reader.py

@@ -55,6 +55,10 @@ def read_gem(
     """
     Read the Stereo-seq GEM file, and generate the StereoExpData object.
 
+    .. seealso::
+
+        `st.io.read_gef <stereo.io.read_gef.html>`_
+
     Parameters
     -------------
     file_path
@@ -475,6 +479,10 @@ def read_h5ms(file_path, use_raw=True, use_result=True):
     """
     Load a h5ms file as an object of MSData
 
+    .. seealso::
+
+        `st.io.write_h5ms <stereo.io.write_h5ms.html>`_
+
     :param file_path: The path of h5ms file to be loaded.
     :param use_raw: Whether to load the raw data of each StereoExpData in MSData, defaults to True.
     :param use_result: Whether to load the analysis results which had been saved in h5ms file, defaults to True.
@@ -754,7 +762,13 @@ def read_h5ad(
         **kwargs
 ) -> Union[StereoExpData, AnnBasedStereoExpData]:
     """
-    Read a h5ad file or load a AnnData object
+    Read a h5 file or load an AnnData object.
+
+    .. seealso::
+
+        `st.io.write_h5ad <stereo.io.write_h5ad.html>`_
+
+        `st.io.stereo_to_anndata <stereo.io.stereo_to_anndata.html>`_
 
     Parameters
     ------------------
@@ -765,8 +779,8 @@ def read_h5ad(
         `file_path` and `anndata` only can input one of them.
     flavor
         the format of the h5ad file, defaults to `'scanpy'`.
-        `scanpy`: AnnData format of scanpy
-        `stereopy`: h5 format of stereo
+        `scanpy`: h5 format of AnnData
+        `stereopy`: h5 format of StereoExpData
     bin_type
         the bin type includes `'bins'` and `'cell_bins'`.
     bin_size
@@ -870,6 +884,12 @@ def stereo_to_anndata(
     """
     Transform the StereoExpData object into Anndata format.
 
+    .. seealso::
+
+        `st.io.read_h5ad <stereo.io.read_h5ad.html>`_
+
+        `st.io.write_h5ad <stereo.io.write_h5ad.html>`_
+
     Parameters
     -----------------------
     data
@@ -1270,6 +1290,10 @@ def read_gef(
     """
     Read the GEF (.h5) file, and generate the StereoExpData object.
 
+    .. seealso::
+
+        `st.io.read_gem <stereo.io.read_gem.html>`_
+
     Parameters
     ---------------
     file_path
@@ -1560,6 +1584,10 @@ def mudata_to_msdata(
     """
     Read a h5mu file and convert it to a MSData object.
 
+    .. seealso::
+
+        `st.io.write_h5mu <stereo.io.write_h5mu.html>`_
+
     :param file_path: The path of the MuData file, defaults to None
     :param sample_names: The names of single samples that are saved in the MuData object, defaults to None,
                             if None, the names starting with 'sample_' will be used.

stereo/io/writer.py

@@ -43,7 +43,19 @@ def write_h5ad(
         output: str = None,
         split_batches: bool = True):
     """
-    Write the StereoExpData into a H5ad file.
+    Write the **StereoExpData** object into a h5 file, we recommend you to set the suffix of the file as **.h5st**.
+    
+    This is a specific format for **StereoExpData** object, not the format of **AnnData** which is suffixed with **.h5ad**.
+
+    When reading it back using `st.io.read_h5ad`, the parameter `flavor` should be set to **'stereopy'**.
+
+    If you want to save the **StereoExpData** object into a **.h5ad** file, you can use `st.io.stereo_to_anndata`.
+
+    .. seealso::
+
+        `st.io.read_h5ad <stereo.io.read_h5ad.html>`_
+        
+        `st.io.stereo_to_anndata <stereo.io.stereo_to_anndata.html>`_
 
     Parameters
     ---------------------
@@ -333,6 +345,10 @@ def write_h5ms(ms_data, output: str, anndata_as_anndata: bool = True):
     """
     Save an object of MSData into a h5 file whose suffix is 'h5ms'.
 
+    .. seealso::
+
+        `st.io.read_h5ms <stereo.io.read_h5ms.html>`_
+
     :param ms_data: The object of MSData to be saved.
     :param output: The path of file into which MSData is saved.
     """
@@ -538,6 +554,10 @@ def write_h5mu(ms_data: MSData, output: str = None, compression: Optional[Litera
     """
     Convert the MSData to a MuData and save it as a h5mu file.
 
+    .. seealso::
+
+        `st.io.mudata_to_msdata <stereo.io.mudata_to_msdata.html>`_
+
     The single samples saved in MSData.data_list are named as 'sample_{i}'.
     The scope data merged from some samples are named starting with 'scope_[{i0,i1,i2...}]'.