update docs

lilab-bcb · Jul 5, 2022 · 868f8f6 · 868f8f6
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diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -32,6 +32,7 @@ Preprocess
     filter_data
     identify_robust_genes
     log_norm
+    arcsinh_transform
     highly_variable_features
     select_features
     pca
@@ -164,6 +165,7 @@ Plotting
     ridgeplot
     wordcloud
     plot_gsea
+    elbowplot
 
 Pseudo-bulk analysis
 ---------------------

diff --git a/docs/conf.py b/docs/conf.py
@@ -29,9 +29,9 @@
 )
 
 # The short X.Y version
-version = "1.6"
+version = "1.7"
 # The full version, including alpha/beta/rc tags
-release = "1.6.0"
+release = "1.7.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -83,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/docs/index.rst b/docs/index.rst
@@ -10,7 +10,7 @@
 Release Highlights in Current Stable
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. include:: release_notes/version_1_6.rst
+.. include:: release_notes/version_1_7.rst
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -6,6 +6,11 @@ Release Notes
 .. note::
     Also see the release notes of `PegasusIO <https://pegasusio.readthedocs.io/en/stable/release_notes.html>`__.
 
+Version 1.7
+~~~~~~~~~~~~~
+
+.. include:: release_notes/version_1_7.rst
+
 Version 1.6
 ~~~~~~~~~~~~~
 

diff --git a/docs/release_notes/version_1_7.rst b/docs/release_notes/version_1_7.rst
@@ -0,0 +1,12 @@
+1.7.0 :small:`July 5, 2022`
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**New Features**
+
+* Add `pegasus.elbowplot <./api/pegasus.elbowplot.html>`_ function to generate elbowplot, with an automated suggestion on number of PCs to be selected based on random matrix theory (`[Johnstone 2001] <https://projecteuclid.org/journals/annals-of-statistics/volume-29/issue-2/On-the-distribution-of-the-largest-eigenvalue-in-principal/10.1214/aos/1009210544.full>`_ and `[Shekhar 2022] <https://elifesciences.org/articles/73809>`_).
+* Add `arcsinh_transform <./api/pegasus.arcsinh_transform.html>`_ function for arcsinh transformation on the count matrix.
+
+**API Changes**
+
+* Function ``nearest_neighbors`` has additional argument ``n_comps`` to allow use part of the components from the source embedding for calculating the nearest neighbor graph.
+* Add ``n_comps`` argument for ``run_harmony``, ``tsne``, ``umap``, and ``fle`` (argument name is ``rep_ncomps``) functions to allow select part of the components from the source embedding.
diff --git a/pegasus/tools/visualization.py b/pegasus/tools/visualization.py
@@ -419,7 +419,7 @@ def fle(
     rep: ``str``, optional, default: ``"diffmap"``
         Representation of data used for the calculation. By default, use Diffusion Map coordinates. If ``None``, use the count matrix ``data.X``.
 
-    rep_ncomps: `int`, optional (default: None)
+    rep_ncomps: ``int``, optional (default: None)
         Number of components to be used in `rep`. If rep_ncomps == None, use all components; otherwise, use the minimum of rep_ncomps and rep's dimensions.
 
     K: ``int``, optional, default: ``50``