remove colorbar if legend_loc=None for continuous colorbars (scverse#…

…1821) * remove colorbar im legend_loc is None for continuous colorbars * add show_colorbar argument to scatterplots * Rework arg, add test * Release note Co-authored-by: Isaac Virshup <[email protected]>
adamcatto · Mar 31, 2022 · 19d2ab2 · 19d2ab2
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Showing 5 changed files with 19 additions and 3 deletions.
diff --git a/docs/release-notes/1.9.0.md b/docs/release-notes/1.9.0.md
@@ -9,6 +9,7 @@
 - `_choose_representation` now subsets the provided representation to n_pcs, regardless of the name of the provided representation (should affect mostly {func}`~scanpy.pp.neighbors`)  {pr}`2179`  {smaller}`I Virshup` {smaller}`PG Majev`
 - Embedding plots now have a `dimensions` argument, which lets users select which dimensions of their embedding to plot and uses the same broadcasting rules as other arguments {pr}`1538` {smaller}`I Virshup`
 - Number of variables plotted with {func}`~scanpy.pl.pca_loadings` can now be controlled with `n_points` argument. Additionally, variables are no longer repeated if the anndata has less than 30 variables {pr}`2075` {smaller}`Yves33`
+- Embedding plots can now pass `colorbar_loc` to specify the location of colorbar legend, or pass `None` to not show a colorbar {pr}`1821` {smaller}`A Schaar` {smaller}`I Virshup`
 
 ```{rubric} Experimental module
 ```

diff --git a/scanpy/plotting/_docs.py b/scanpy/plotting/_docs.py
@@ -73,6 +73,9 @@
 legend_fontoutline
     Line width of the legend font outline in pt. Draws a white outline using
     the path effect :class:`~matplotlib.patheffects.withStroke`.
+colorbar_loc
+    Where to place the colorbar for continous variables. If `None`, no colorbar
+    is added.
 size
     Point size. If `None`, is automatically computed as 120000 / n_cells.
     Can be a sequence containing the size for each cell. The order should be

diff --git a/scanpy/plotting/_tools/scatterplots.py b/scanpy/plotting/_tools/scatterplots.py
@@ -89,6 +89,7 @@ def embedding(
     legend_fontweight: Union[int, _FontWeight] = 'bold',
     legend_loc: str = 'right margin',
     legend_fontoutline: Optional[int] = None,
+    colorbar_loc: Optional[str] = "right",
     vmax: Union[VBound, Sequence[VBound], None] = None,
     vmin: Union[VBound, Sequence[VBound], None] = None,
     vcenter: Union[VBound, Sequence[VBound], None] = None,
@@ -447,9 +448,10 @@ def embedding(
                 na_in_legend=na_in_legend,
                 multi_panel=bool(grid),
             )
-        else:
-            # TODO: na_in_legend should have some effect here
-            pl.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30)
+        elif colorbar_loc is not None:
+            pl.colorbar(
+                cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=colorbar_loc
+            )
 
     if return_fig is True:
         return fig

diff --git a/scanpy/tests/_images/master_no_colorbar.png b/scanpy/tests/_images/master_no_colorbar.png
diff --git a/scanpy/tests/test_embedding_plots.py b/scanpy/tests/test_embedding_plots.py
@@ -12,6 +12,7 @@
 import scanpy as sc
 
 from scanpy.tests.test_plotting import ROOT, FIGS, HERE
+import scanpy.tests._data._cached_datasets as datasets
 
 MISSING_VALUES_ROOT = ROOT / "embedding-missing-values"
 MISSING_VALUES_FIGS = FIGS / "embedding-missing-values"
@@ -272,6 +273,15 @@ def test_dimensions_same_as_components(adata, tmpdir, check_same_image):
     check_same_image(dims_pth, comp_pth, tol=5)
 
 
+def test_embedding_colorbar_location(image_comparer):
+    save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
+    adata = datasets.pbmc3k_processed().raw.to_adata()
+
+    sc.pl.pca(adata, color="LDHB", colorbar_loc=None)
+
+    save_and_compare_images("master_no_colorbar")
+
+
 # Spatial specific