Merge branch 'main' of https://github.com/theislab/pertpy

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
  hooks:
  - id: prettier
  - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.4.5
+ rev: v0.4.7
  hooks:
  - id: ruff
  args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

pertpy/tools/_differential_gene_expression/_base.py

@@ -257,13 +257,11 @@ def _map_genes_categories_highlight(
  print("0s encountered for p value, replacing with 1e-323")
  df.loc[df[pvalue_col] == 0, pvalue_col] = 1e-323
 
- # max for y-axis
- max_log2fc = df[log2fc_col].max()
-
  # convert p value threshold to nlog10
  pval_thresh = -np.log10(pval_thresh)
  # make nlog10 column
  df["nlog10"] = -np.log10(df[pvalue_col])
+ y_max = df["nlog10"].max() + 1
  # make a column to pick top genes
  df["top_genes"] = df["nlog10"] * df[log2fc_col]
 
@@ -401,7 +399,7 @@ def _map_genes_categories_highlight(
 
  # plot vertical and horizontal lines
  if s_curve:
- x = np.arange((log2fc_thresh + 0.000001), max_log2fc + 1, 0.01)
+ x = np.arange((log2fc_thresh + 0.000001), y_max, 0.01)
  y = _pval_reciprocal(x)
  ax.plot(x, y, zorder=1, c="k", lw=2, ls="--")
  ax.plot(-x, y, zorder=1, c="k", lw=2, ls="--")
@@ -410,7 +408,7 @@ def _map_genes_categories_highlight(
  ax.axhline(pval_thresh, zorder=1, c="k", lw=2, ls="--")
  ax.axvline(log2fc_thresh, zorder=1, c="k", lw=2, ls="--")
  ax.axvline(log2fc_thresh * -1, zorder=1, c="k", lw=2, ls="--")
- plt.ylim(0, max_log2fc + 1)
+ plt.ylim(0, y_max)
  ax.xaxis.set_major_locator(MaxNLocator(integer=True))
 
  # make labels
@@ -437,7 +435,7 @@ def _map_genes_categories_highlight(
  ax.spines["right"].set_visible(False)
 
  ax.tick_params(width=2)
- plt.xticks(size=11)
+ plt.xticks(size=11, fontsize=10)
  plt.yticks(size=11)
 
  # Set default axis titles