version 1.2.1

scverse · Jun 8, 2018 · fb50f38 · fb50f38
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diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -28,6 +28,8 @@ Filtering of highly-variable genes, batch-effect correction, per-cell (UMI) norm
    pp.scale
    pp.subsample
    pp.downsample_counts
+
+For visual quality control, also see :func:`~scanpy.api.pl.highest_expr_gens` and :func:`pl.filter_genes_dispersion` :doc:`plotting API <plotting>`.
 
 **Recipes**
 

diff --git a/docs/api/plotting.rst b/docs/api/plotting.rst
@@ -9,6 +9,7 @@ The following describes the plotting submodule of ``scanpy.api``.
 
     See the :ref:`settings` section for some important plotting configurations.
 
+
 Generic
 -------
 
@@ -26,6 +27,19 @@ Thin wrappers for Seaborn [Waskom16]_ functions.
    pl.violin
    pl.clustermap
 
+
+Preprocessing
+-------------
+
+Methods for visualizing quality control and results of preprocessing functions.
+
+.. autosummary::
+   :toctree: .
+
+   pl.highest_expr_genes
+   pl.filter_genes_dispersion
+
+
 Tools
 -----
 

diff --git a/docs/references.rst b/docs/references.rst
@@ -95,6 +95,10 @@ References
    *Visualizing data using t-SNE*,
    `JMLR <http://www.jmlr.org/papers/v9/vandermaaten08a.html>`_.
 
+.. [McCarthy17] McCarthy *et al.* (2017),
+   *scater: Single-cell analysis toolkit for gene expression data in R*,
+   `Bioinformatics <https://doi.org/10.1093/bioinformatics/btw777>`_.
+
 .. [Moon17] Moon *et al.* (2017),
    *PHATE: A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data*,
    `BioRxiv <http://biorxiv.org/content/early/2017/03/24/120378>`_.

diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -5,6 +5,12 @@
 .. role:: small
 
 
+Version 1.2.1 :small:`June 9, 2018`
+-----------------------------------
+
+- :func:`pl.highest_expr_genes` for quality control, plot genes with highest mean fraction of cells, similar to plotQC of *Scater* [McCarthy17]_
+
+
 Version 1.2 :small:`June 8, 2018`
 ---------------------------------