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Add smallest_dot parameter to dotplot #524

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Merged
falexwolf merged 1 commit into from
Mar 11, 2019
Merged

Add smallest_dot parameter to dotplot #524

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7 changes: 6 additions & 1 deletion scanpy/plotting/_anndata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1305,7 +1305,7 @@ def heatmap(adata, var_names, groupby=None, use_raw=None, log=False, num_categor
@doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
def dotplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categories=7,
color_map='Reds', dot_max=None, dot_min=None, figsize=None, dendrogram=False,
gene_symbols=None, var_group_positions=None,
gene_symbols=None, var_group_positions=None, smallest_dot=0.,
var_group_labels=None, var_group_rotation=None, layer=None, show=None, save=None, **kwds):
"""\
Makes a *dot plot* of the expression values of `var_names`.
Expand Down Expand Up @@ -1334,6 +1334,9 @@ def dotplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categor
If none, the minimum dot size is set to 0. If given,
the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to
this value.
smallest_dot : `float` optional (default: 0.)
If none, the smallest dot has size 0. All expression levels with `dot_min` are potted with
`smallest_dot` dot size.

{show_save_ax}
**kwds : keyword arguments
Expand Down Expand Up @@ -1489,6 +1492,7 @@ def dotplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categor
frac = ((frac - dot_min) / old_range)

size = (frac * 10) ** 2
size += smallest_dot
import matplotlib.colors

normalize = matplotlib.colors.Normalize(vmin=kwds.get('vmin'), vmax=kwds.get('vmax'))
Expand Down Expand Up @@ -1542,6 +1546,7 @@ def dotplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categor
else:
fracs_values = fracs_legends
size = (fracs_values * 10) ** 2
size += smallest_dot
color = [cmap(normalize(value)) for value in np.repeat(max(mean_flat) * 0.7, len(size))]

# plot size bar
Expand Down