Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barp…

…lot (#667)

pertpy/tools/_coda/_base_coda.py

@@ -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,

pertpy/tools/_mixscape.py

@@ -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:
@@ -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:
@@ -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 = (
@@ -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",
@@ -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)
@@ -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:
@@ -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