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Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot #667

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merged 1 commit into from
Oct 11, 2024
Merged

Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot #667

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1 change: 0 additions & 1 deletion pertpy/tools/_coda/_base_coda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1378,7 +1378,6 @@ def plot_effects_barplot( # pragma: no cover
if len(covariate_names_zero) != 0:
if plot_facets:
if plot_zero_covariate and not plot_zero_cell_type:
plot_df = plot_df[plot_df["value"] != 0]
for covariate_name_zero in covariate_names_zero:
new_row = {
"Covariate": covariate_name_zero,
Expand Down
33 changes: 15 additions & 18 deletions pertpy/tools/_mixscape.py
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Original file line number Diff line number Diff line change
Expand Up @@ -521,6 +521,7 @@ def plot_barplot( # pragma: no cover
legend_title_size: int = 8,
legend_text_size: int = 8,
legend_bbox_to_anchor: tuple[float, float] = None,
figsize: tuple[float, float] = (25, 25),
show: bool = True,
return_fig: bool = False,
) -> Figure | None:
Expand All @@ -537,6 +538,7 @@ def plot_barplot( # pragma: no cover
legend_title_size: Size of the legend title.
legend_text_size: Size of the legend text.
legend_bbox_to_anchor: The bbox that the legend will be anchored.
figsize: The size of the figure.
{common_plot_args}

Returns:
Expand Down Expand Up @@ -574,7 +576,7 @@ def plot_barplot( # pragma: no cover

color_mapping = {"KO": "salmon", "NP": "lightgray", "NT": "grey"}
unique_genes = NP_KO_cells["gene"].unique()
fig, axs = plt.subplots(int(len(unique_genes) / 5), 5, figsize=(25, 25), sharey=True)
fig, axs = plt.subplots(int(len(unique_genes) / 5), 5, figsize=figsize, sharey=True)
for i, gene in enumerate(unique_genes):
ax = axs[int(i / 5), i % 5]
grouped_df = (
Expand All @@ -594,11 +596,8 @@ def plot_barplot( # pragma: no cover
ax.set_title(gene, bbox={"facecolor": "white", "edgecolor": "black", "pad": 1}, fontsize=axis_title_size)
ax.set(xlabel="sgRNA", ylabel="% of cells")
sns.despine(ax=ax, top=True, right=True, left=False, bottom=False)
ax.set_xticklabels(ax.get_xticklabels(), rotation=0, ha="right", fontsize=axis_text_x_size)
ax.set_yticklabels(ax.get_yticklabels(), rotation=0, fontsize=axis_text_y_size)

fig.subplots_adjust(right=0.8)
fig.subplots_adjust(hspace=0.5, wspace=0.5)
ax.set_xticks(ax.get_xticks(),ax.get_xticklabels(), rotation=0, ha="right", fontsize=axis_text_x_size)
ax.set_yticks(ax.get_yticks(), ax.get_yticklabels(), rotation=0, fontsize=axis_text_y_size)
ax.legend(
title="Mixscape Class",
loc="center right",
Expand All @@ -608,10 +607,14 @@ def plot_barplot( # pragma: no cover
title_fontsize=legend_title_size,
)

fig.subplots_adjust(right=0.8)
fig.subplots_adjust(hspace=0.5, wspace=0.5)
plt.tight_layout()

if show:
plt.show()
if return_fig:
return plt.gcf()
return fig
return None

@_doc_params(common_plot_args=doc_common_plot_args)
Expand Down Expand Up @@ -792,12 +795,6 @@ def plot_perturbscore( # pragma: no cover
plt.legend(title="gene_target", title_fontsize=14, fontsize=12)
sns.despine()

if show:
plt.show()
if return_fig:
return plt.gcf()
return None

# If before_mixscape is False, split densities based on mixscape classifications
else:
if palette is None:
Expand Down Expand Up @@ -854,11 +851,11 @@ def plot_perturbscore( # pragma: no cover
plt.legend(title="mixscape class", title_fontsize=14, fontsize=12)
sns.despine()

if show:
plt.show()
if return_fig:
return plt.gcf()
return None
if show:
plt.show()
if return_fig:
return plt.gcf()
return None

@_doc_params(common_plot_args=doc_common_plot_args)
def plot_violin( # pragma: no cover
Expand Down
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