Release/0.2.4.post1 (#50)

* Feature/plot paga (#48) * Make plot paga overlay paga on arbitrary cell embeddings * Fix test * Fix "--svd-solver=auto" * Add "--edge-width-scale" (#49) * Add "--edge-width-scale" * Add test for "--edge-width-scale" * Bump version
ebi-gene-expression-group · Aug 29, 2019 · 96308e9 · 96308e9
1 parent 4a3f918
commit 96308e9
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diff --git a/scanpy-scripts-tests.bats b/scanpy-scripts-tests.bats
@@ -23,7 +23,7 @@ setup() {
     scale_opt="-m 10 --show-obj stdout"
     scale_obj="${output_dir}/scale.h5ad"
     pca_embed="${output_dir}/pca.tsv"
-    pca_opt="--n-comps 50 -V arpack --show-obj stdout -E ${pca_embed}"
+    pca_opt="--n-comps 50 -V auto --show-obj stdout -E ${pca_embed}"
     pca_obj="${output_dir}/pca.h5ad"
     neighbor_opt="-k 5,10,20 -n 25 -m umap --show-obj stdout"
     neighbor_obj="${output_dir}/neighbor.h5ad"
@@ -46,13 +46,13 @@ setup() {
     paga_opt="--use-graph neighbors_k10 --key-added k10_r0_7 --groups leiden_k10_r0_7 --model v1.2 -f loom"
     paga_obj="${output_dir}/paga.h5ad"
     diffmap_embed="${output_dir}/diffmap.tsv"
-    diffmap_opt="--use-graph neighbors_k10 --n-comps 10 -E ${diffmap_embed} -f loom"
+    diffmap_opt="--use-graph neighbors_k10 --n-comps 10 -E ${diffmap_embed}"
     diffmap_obj="${output_dir}/diffmap.h5ad"
     dpt_opt="--use-graph neighbors_k10 --key-added k10 --n-dcs 10 --root leiden_k10_r0_7 0"
     dpt_obj="${output_dir}/dpt.h5ad"
     plt_embed_opt="--color leiden_k10_r0_7 -f loom"
     plt_embed_pdf="${output_dir}/umap_leiden_k10_r0_7.pdf"
-    plt_paga_opt="--use-key paga_k10_r0_7 --node-size-scale 2"
+    plt_paga_opt="--use-key paga_k10_r0_7 --node-size-scale 2 --edge-width-scale 0.5 --basis diffmap --color dpt_pseudotime_k10 --frameoff"
     plt_paga_pdf="${output_dir}/paga_k10_r0_7.pdf"
 
     if [ ! -d "$data_dir" ]; then
@@ -277,7 +277,7 @@ setup() {
         skip "$diffmap_obj exists and resume is set to 'true'"
     fi
 
-    run rm -f $diffmap_obj && $scanpy embed diffmap $diffmap_opt $leiden_obj $diffmap_obj
+    run rm -f $diffmap_obj && $scanpy embed diffmap $diffmap_opt $paga_obj $diffmap_obj
 
     [ "$status" -eq 0 ]
     [ -f  "$diffmap_obj" ] && [ -f "$diffmap_embed" ]
@@ -316,7 +316,7 @@ setup() {
         skip "$plt_paga_pdf exists and resume is set to 'true'"
     fi
 
-    run rm -f $plt_paga_pdf && $scanpy plot paga $plt_paga_opt $paga_obj $plt_paga_pdf
+    run rm -f $plt_paga_pdf && $scanpy plot paga $plt_paga_opt $dpt_obj $plt_paga_pdf
 
     [ "$status" -eq 0 ]
     [ -f  "$dpt_obj" ]

diff --git a/scanpy_scripts/cmd_options.py b/scanpy_scripts/cmd_options.py
@@ -930,14 +930,6 @@
 PLOT_PAGA_CMD_OPTIONS = [
     *COMMON_OPTIONS['input'],
     *COMMON_OPTIONS['plot'],
-    COMMON_OPTIONS['random_state'],
-    click.option(
-        '--type', 'prefix',
-        type=click.Choice(['paga', 'paga_compare']),
-        default='paga',
-        show_default=True,
-        help='The type of visualisation.',
-    ),
     click.option(
         '--use-key',
         type=click.STRING,
@@ -997,12 +989,35 @@
         help='Key for `.uns["paga"]` that specifies the matrix that stores the '
         'edges to be drawn solid black.',
     ),
+    click.option(
+        '--basis',
+        type=click.STRING,
+        default=None,
+        show_default=True,
+        help='Name of the embedding to plot, must be a key of `.obsm` without '
+        'the prefix "X_".',
+    ),
     click.option(
         '--color',
-        type=CommaSeparatedText(simplify=True),
+        type=click.STRING,
         default=None,
         show_default=True,
-        help='Keys for annotations of observations/cells or variables/genes.',
+        help='Key for annotation of observations/cells or variables/genes.',
+    ),
+    click.option(
+        '--legend-loc',
+        type=click.Choice(['right margin', 'on data']),
+        default='right margin',
+        show_default=True,
+        help='Location of legend, either "on data", "right margin" or valid '
+        'keywords for `matplotlib.legend`.',
+    ),
+    click.option(
+        '--size',
+        type=click.FLOAT,
+        default=None,
+        show_default=True,
+        help='Point size. Automatically computed if not specified.',
     ),
     click.option(
         '--node-size-scale',
@@ -1016,13 +1031,20 @@
         type=click.INT,
         default=None,
         show_default=True,
-        help='Font size for node labels',
+        help='Font size for node labels.',
+    ),
+    click.option(
+        '--edge-width-scale',
+        type=click.FLOAT,
+        default=1.0,
+        show_default=True,
+        help='Increase of decrease the width of the edges.',
     ),
     click.option(
         '--arrowsize',
         type=click.INT,
         default=30,
         show_default=True,
-        help='For directed graphs, specify the length and width of the arrowhead',
+        help='For directed graphs, specify the length and width of the arrowhead.',
     ),
 ]
diff --git a/scanpy_scripts/cmd_utils.py b/scanpy_scripts/cmd_utils.py
@@ -176,7 +176,7 @@ def write_embedding(adata, key, embed_fn, n_comp=None, sep='\t', key_added=None)
         embed_fn, sep=sep, header=False, index=True)
 
 
-def make_plot_function(FUN):
+def make_plot_function(FUN, kind=None):
     """Make plot function that handles common plotting parameters
     """
     def plot_function(
@@ -199,7 +199,7 @@ def plot_function(
         if output_fig:
             import os
             import matplotlib.pyplot as plt
-            sc.settings.figdir = os.path.dirname(output_fig)
+            sc.settings.figdir = os.path.dirname(output_fig) or '.'
 
             figname = os.path.basename(output_fig)
             showfig = False
@@ -213,7 +213,7 @@ def plot_function(
             **kwargs)
 
         if output_fig:
-            prefix = kwargs.get('prefix', kwargs.get('basis', FUN.__name__))
+            prefix = kind if kind else kwargs.get('basis', FUN.__name__)
             os.rename(
                 os.path.join(sc.settings.figdir, prefix + figname), output_fig)
             plt.close()

diff --git a/scanpy_scripts/cmds.py b/scanpy_scripts/cmds.py
@@ -217,7 +217,7 @@
 PLOT_PAGA_CMD = make_subcmd(
     'paga',
     PLOT_PAGA_CMD_OPTIONS,
-    make_plot_function(plot_paga),
+    make_plot_function(plot_paga, kind='paga'),
     cmd_desc='Plot PAGA trajectories.',
     arg_desc=_IP_DESC,
 )
diff --git a/scanpy_scripts/lib/__init__.py b/scanpy_scripts/lib/__init__.py
@@ -15,6 +15,6 @@
 from ._diffexp import diffexp, diffexp_paired, extract_de_table
 from ._diffmap import diffmap
 from ._dpt import dpt
-from ._paga import paga
+from ._paga import paga, plot_paga
 from ..cmd_utils import _read_obj as read_obj
 from ..cmd_utils import _write_obj as write_obj
diff --git a/scanpy_scripts/lib/_paga.py b/scanpy_scripts/lib/_paga.py
@@ -2,6 +2,7 @@
 scanpy paga
 """
 
+import numpy as np
 import scanpy as sc
 from ..cmd_utils import (
     _backup_default_key,
@@ -39,17 +40,69 @@ def paga(
 
 def plot_paga(
         adata,
-        prefix='paga',
         use_key='paga',
+        basis=None,
+        layout=None,
+        init_pos=None,
+        legend_loc='on data',
+        color=None,
+        size=None,
+        title=None,
+        show=None,
+        save=None,
         **kwargs,
 ):
     """Make PAGA plot
     """
-    _set_default_key(adata.uns, 'paga', use_key)
-    if prefix == 'paga':
-        sc.pl.paga(adata, **kwargs)
-    elif prefix == 'paga_compare':
-        sc.pl.paga_compare(adata, **kwargs)
+    if basis is not None and f'X_{basis}' in adata.obsm.keys():
+        ax = sc.plotting._tools.scatterplots.plot_scatter(
+            adata,
+            basis=basis,
+            color=color,
+            legend_loc=legend_loc,
+            size=size,
+            title=None,
+            save=False,
+            show=False,
+        )
+
+        grouping = adata.uns[use_key]['groups']
+        categories = list(adata.obs[grouping].cat.categories)
+        obsm = adata.obsm[f'X_{basis}']
+        group_pos = np.zeros((len(categories), 2))
+        for i, label in enumerate(categories):
+            offset = 1 if basis.startswith('diffmap') else 0
+            _scatter = obsm[adata.obs[grouping] == label, (0+offset):(2+offset)]
+            x_pos, y_pos = np.median(_scatter, axis=0)
+            group_pos[i] = [x_pos, y_pos]
+
+        _set_default_key(adata.uns, 'paga', use_key)
+        kwargs['node_size_scale'] = 0
+        kwargs['fontsize'] = 1
+        kwargs['pos'] = group_pos
+        kwargs['color'] = None
+        try:
+            sc.pl.paga(
+                adata,
+                ax=ax,
+                title=title,
+                show=show,
+                save=save,
+                **kwargs,
+            )
+        finally:
+            _restore_default_key(adata.uns, 'paga', use_key)
     else:
-        raise ValueError(f'{prefix}: unknown plot type for PAGA')
-    _restore_default_key(adata.uns, 'paga', use_key)
+        _set_default_key(adata.uns, 'paga', use_key)
+        try:
+            sc.pl.paga(
+                adata,
+                layout=layout,
+                init_pos=init_pos,
+                title=title,
+                show=show,
+                save=save,
+                **kwargs
+            )
+        finally:
+            _restore_default_key(adata.uns, 'paga', use_key)
diff --git a/scanpy_scripts/lib/_pca.py b/scanpy_scripts/lib/_pca.py
@@ -9,6 +9,10 @@ def pca(adata, key_added=None, export_embedding=None, **kwargs):
     """
     Wrapper function for sc.pp.pca, for supporting named slot
     """
+    # omit "svd_solver" to let scanpy choose automatically
+    if 'svd_solver' in kwargs and kwargs['svd_solver'] == 'auto':
+        del kwargs['svd_solver']
+
     if key_added:
         if 'X_pca' in adata.obsm.keys():
             adata.obsm['X_pca_bkup'] = adata.obsm['X_pca']

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setup(
     name='scanpy-scripts',
-    version='0.2.4',
+    version='0.2.4.post1',
     author='nh3',
     author_email='[email protected]',
     description='Scripts for using scanpy from the command line',