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Merged
RicardoRyn merged 2 commits into from
Dec 8, 2025
Merged

Push ywprpvtunupp #62

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144f44e
feat(bar): add customizable y_base and interval for significance anno…
RicardoRyn Dec 5, 2025
2a54572
chore(docs): simplify zensical configuration and remove tests
RicardoRyn Dec 5, 2025
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8 changes: 0 additions & 8 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,8 @@ wheels/
# Virtual environments
.venv

# Figures
notebooks/example_data/
tests/figures/

# deployment
site/

# ai agent docs
IFLOW.md

*.bak
.vscode/

60 changes: 44 additions & 16 deletions src/plotfig/bar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@
]



def _is_valid_data(data):
if isinstance(data, np.ndarray):
return data.ndim == 2
Expand Down Expand Up @@ -225,6 +224,8 @@ def _statistics(
statistical_line_color,
asterisk_fontsize,
asterisk_color,
y_base,
interval,
):
if isinstance(test_method, list):
if len(test_method) > 2 or (
Expand All @@ -240,7 +241,8 @@ def _statistics(
return

y_max = ax.get_ylim()[1]
interval = (y_max - np.max(all_values)) / (len(comparisons) + 1)
y_base = y_base or np.max(all_values)
interval = interval or (y_max - np.max(all_values)) / (len(comparisons) + 1)

color = (
"b"
Expand All @@ -251,7 +253,7 @@ def _statistics(
_annotate_significance(
ax,
comparisons,
np.max(all_values),
y_base,
interval,
line_color=statistical_line_color,
star_offset=interval / 5,
Expand All @@ -269,11 +271,13 @@ def _statistics(
return

y_max = ax.get_ylim()[1]
interval = (y_max - np.max(all_values)) / (len(comparisons) + 1)
y_base = y_base or np.max(all_values)
interval = interval or (y_max - np.max(all_values)) / (len(comparisons) + 1)

_annotate_significance(
ax,
comparisons,
np.max(all_values),
y_base,
interval,
line_color=statistical_line_color,
star_offset=interval / 5,
Expand All @@ -293,7 +297,6 @@ def plot_one_group_bar_figure(
colors_end: list[str] | None = None,
show_dots: bool = True,
dots_color: list[list[str]] | None = None,
y_lim: list[Num] | tuple[Num, Num] | None = None,
width: Num = 0.5,
color_alpha: Num = 1,
dots_size: Num = 35,
Expand All @@ -310,13 +313,16 @@ def plot_one_group_bar_figure(
y_label_fontsize: Num = 10,
y_tick_fontsize: Num = 8,
y_tick_rotation: Num = 0,
y_lim: list[Num] | tuple[Num, Num] | None = None,
statistic: bool = False,
test_method: list[str] = ["ttest_ind"],
p_list: list[float] | None = None,
popmean: Num = 0,
statistical_line_color: str = "0.5",
asterisk_fontsize: Num = 10,
asterisk_color: str = "k",
y_base: float | None = None,
interval: float | None = None,
ax_bottom_is_0: bool = False,
y_max_tick_is_1: bool = False,
math_text: bool = True,
Expand Down Expand Up @@ -346,8 +352,6 @@ def plot_one_group_bar_figure(
是否显示散点. Defaults to True.
dots_color (list[list[str]] | None, optional):
散点的颜色列表. Defaults to None.
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
width (Num, optional):
柱状图的宽度. Defaults to 0.5.
color_alpha (Num, optional):
Expand Down Expand Up @@ -380,6 +384,8 @@ def plot_one_group_bar_figure(
Y轴刻度字体大小. Defaults to 8.
y_tick_rotation (Num, optional):
Y轴刻度旋转角度. Defaults to 0.
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
statistic (bool, optional):
是否进行统计显著性分析. Defaults to False.
test_method (list[str], optional):
Expand All @@ -400,6 +406,10 @@ def plot_one_group_bar_figure(
显著性星号的字体大小. Defaults to 10.
asterisk_color (str, optional):
显著性星号的颜色. Defaults to "k".
y_base (float | None, optional):
显著性连线的起始Y轴位置（高度）。如果为None，则使用内部算法自动计算一个合适的位置。Defaults to None.
interval (float | None, optional):
相邻显著性连线之间的垂直距离（Y轴增量）。如果为None，则使用内部算法根据图表范围和比较对数自动计算。Defaults to None.
ax_bottom_is_0 (bool, optional):
Y轴是否从0开始. Defaults to False.
y_max_tick_is_1 (bool, optional):
Expand Down Expand Up @@ -549,6 +559,8 @@ def plot_one_group_bar_figure(
statistical_line_color,
asterisk_fontsize,
asterisk_color,
y_base,
interval,
)
return ax

Expand Down Expand Up @@ -577,14 +589,16 @@ def plot_one_group_violin_figure(
y_label_fontsize: Num = 10,
y_tick_fontsize: Num = 8,
y_tick_rotation: Num = 0,
y_lim: list[Num] | tuple[Num, Num] | None = None,
statistic: bool = False,
test_method: list[str] = ["ttest_ind"],
popmean: Num = 0,
p_list: list[float] | None = None,
statistical_line_color: str = "0.5",
asterisk_fontsize: Num = 10,
asterisk_color: str = "k",
y_lim: list[Num] | tuple[Num, Num] | None = None,
y_base: float | None = None,
interval: float | None = None,
ax_bottom_is_0: bool = False,
y_max_tick_is_1: bool = False,
math_text: bool = True,
Expand Down Expand Up @@ -640,6 +654,8 @@ def plot_one_group_violin_figure(
Y轴刻度字体大小. Defaults to 8.
y_tick_rotation (Num, optional):
Y轴刻度旋转角度. Defaults to 0.
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
statistic (bool, optional):
是否进行统计显著性分析. Defaults to False.
test_method (list[str], optional):
Expand All @@ -654,8 +670,10 @@ def plot_one_group_violin_figure(
显著性星号的字体大小. Defaults to 10.
asterisk_color (str, optional):
显著性星号的颜色. Defaults to "k".
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
y_base (float | None, optional):
显著性连线的起始Y轴位置（高度）。如果为None，则使用内部算法自动计算一个合适的位置。Defaults to None.
interval (float | None, optional):
相邻显著性连线之间的垂直距离（Y轴增量）。如果为None，则使用内部算法根据图表范围和比较对数自动计算。Defaults to None.
ax_bottom_is_0 (bool, optional):
Y轴是否从0开始. Defaults to False.
y_max_tick_is_1 (bool, optional):
Expand Down Expand Up @@ -830,6 +848,8 @@ def _draw_gradient_violin(ax, data, pos, width, c1, c2, color_alpha):
statistical_line_color,
asterisk_fontsize,
asterisk_color,
y_base,
interval,
)

return ax
Expand Down Expand Up @@ -860,13 +880,15 @@ def plot_multi_group_bar_figure(
y_label_fontsize=10,
y_tick_fontsize=8,
y_tick_rotation=0,
y_lim: list[Num] | tuple[Num, Num] | None = None,
statistic: bool = False,
test_method: str = "external",
p_list: list[list[Num]] | None = None,
line_color="0.5",
asterisk_fontsize=10,
asterisk_color="k",
y_lim: list[Num] | tuple[Num, Num] | None = None,
y_base: float | None = None,
interval: float | None = None,
ax_bottom_is_0: bool = False,
y_max_tick_is_1: bool = False,
math_text: bool = True,
Expand Down Expand Up @@ -924,6 +946,8 @@ def plot_multi_group_bar_figure(
Y轴刻度字体大小. Defaults to 8.
y_tick_rotation (int, optional):
Y轴刻度旋转角度. Defaults to 0.
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
statistic (bool, optional):
是否进行统计显著性分析. Defaults to False.
test_method (str, optional):
Expand All @@ -936,8 +960,10 @@ def plot_multi_group_bar_figure(
显著性星号的字体大小. Defaults to 10.
asterisk_color (str, optional):
显著性星号的颜色. Defaults to "k".
y_lim (list[Num] | tuple[Num, Num] | None, optional):
Y轴的范围限制. Defaults to None.
y_base (float | None, optional):
显著性连线的起始Y轴位置（高度）。如果为None，则使用内部算法自动计算一个合适的位置。Defaults to None.
interval (float | None, optional):
相邻显著性连线之间的垂直距离（Y轴增量）。如果为None，则使用内部算法根据图表范围和比较对数自动计算。Defaults to None.
ax_bottom_is_0 (bool, optional):
Y轴是否从0开始. Defaults to False.
y_max_tick_is_1 (bool, optional):
Expand Down Expand Up @@ -1067,11 +1093,13 @@ def plot_multi_group_bar_figure(
if p <= 0.05:
comparisons.append((x_positions[i], x_positions[j], p))
y_max = ax.get_ylim()[1]
interval = (y_max - np.max(all_values)) / (len(comparisons) + 1)
y_base = y_base or np.max(all_values)
interval = interval or (y_max - np.max(all_values)) / (len(comparisons) + 1)

_annotate_significance(
ax,
comparisons,
np.max(all_values),
y_base,
interval,
line_color=line_color,
star_offset=interval / 5,
Expand Down
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