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Prop plot docs fix #221

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59b3c8c
SD to BSE update
mnicolee Jul 24, 2026
d413232
Updating the .py files
mnicolee Jul 24, 2026
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2 changes: 1 addition & 1 deletion dabest/_effsize_objects.py
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Expand Up @@ -1304,7 +1304,7 @@ def plot(
group_summaries : ['mean_sd', 'median_quartiles', 'None'], default "mean_sd".
Plots the summary statistics for each group. If 'mean_sd', then
the mean and standard deviation of each group is plotted as a
notched line beside each group. If 'median_quantiles', then the
notched line beside each group. For proportion and Sankey plots, this error is the binomial standard error (BSE), sqrt(p(1-p)/n), not the SD. If 'median_quantiles', then the
median and 25th and 75th percentiles of each group is plotted
instead. If 'None', the summaries are not shown.
fig_size : tuple, default None
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7 changes: 3 additions & 4 deletions dabest/plot_tools.py
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Expand Up @@ -70,7 +70,7 @@ def error_bar(
data: pd.DataFrame, # This DataFrame should be in 'long' format.
x: str, # x column to be plotted.
y: str, # y column to be plotted.
type: str = "mean_sd", # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.
type: str = "mean_sd", # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. For proportion and Sankey plots, the error shown is the binomial standard error (BSE), sqrt(p(1-p)/n), rather than the SD. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.
offset: float = 0.2, # Give a single float (that will be used as the x-offset of all gapped lines), or an iterable containing the list of x-offsets.
ax=None, # If a matplotlib Axes object is specified, the gapped lines will be plotted in order on this axes. If None, the current axes (plt.gca()) is used.
line_color="black", # The color of the gapped lines.
Expand All @@ -85,11 +85,10 @@ def error_bar(
):
"""
Function to plot the standard deviations as vertical errorbars.
For proportion and Sankey plots, the vertical bars instead show the
BSE of the proportion.
The mean is a gap defined by negative space.

This function combines the functionality of gapped_lines(),
proportional_error_bar(), and sankey_error_bar().

"""

if gap_width_percent < 0 or gap_width_percent > 100:
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2 changes: 1 addition & 1 deletion nbs/02-about.ipynb
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Expand Up @@ -32,7 +32,7 @@
"\n",
"- Statistics supervision by Hyungwon Choi\n",
"\n",
"- Alpha testers from the Claridge-Chang lab: [Sangyu Xu](https://github.com/sangyu), [Xianyuan Zhang](https://github.com/XYZfar), [Farhan Mohammad](https://github.com/farhan8igib), Jurga Mituzaitė, Stanislav Ott, Tayfun Tumkaya, Jonathan Anns, Nicole Lee and Yishan Mai.\n",
"- Alpha testers from the Claridge-Chang lab: [Sangyu Xu](https://github.com/sangyu), [Xianyuan Zhang](https://github.com/XYZfar), [Farhan Mohammad](https://github.com/farhan8igib), Jurga Mituzaitė, Stanislav Ott, [Tayfun Tumkaya](https://github.com/ttumkaya), [Jonathan Anns](https://github.com/JAnns98), [Nicole Lee](https://github.com/mnicolee) and [Yishan Mai](https://github.com/maiyishan).\n",
"\n",
"- DizietAsahi ([DizietAsahi](https://github.com/DizietAsahi)) with [PR #86](https://github.com/ACCLAB/DABEST-python/pull/86): Fix bugs in slopegraph and reference line keyword parsing.\n",
"\n",
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2 changes: 1 addition & 1 deletion nbs/API/effsize_objects.ipynb
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Expand Up @@ -1515,7 +1515,7 @@
" group_summaries : ['mean_sd', 'median_quartiles', 'None'], default \"mean_sd\".\n",
" Plots the summary statistics for each group. If 'mean_sd', then\n",
" the mean and standard deviation of each group is plotted as a\n",
" notched line beside each group. If 'median_quantiles', then the\n",
" notched line beside each group. For proportion and Sankey plots, this error is the binomial standard error (BSE), sqrt(p(1-p)/n), not the SD. If 'median_quantiles', then the\n",
" median and 25th and 75th percentiles of each group is plotted\n",
" instead. If 'None', the summaries are not shown.\n",
" fig_size : tuple, default None\n",
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7 changes: 3 additions & 4 deletions nbs/API/plot_tools.ipynb
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Expand Up @@ -121,7 +121,7 @@
" data: pd.DataFrame, # This DataFrame should be in 'long' format.\n",
" x: str, # x column to be plotted.\n",
" y: str, # y column to be plotted.\n",
" type: str = \"mean_sd\", # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.\n",
" type: str = \"mean_sd\", # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. For proportion and Sankey plots, the error shown is the binomial standard error (BSE), sqrt(p(1-p)/n), rather than the SD. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.\n",
" offset: float = 0.2, # Give a single float (that will be used as the x-offset of all gapped lines), or an iterable containing the list of x-offsets.\n",
" ax=None, # If a matplotlib Axes object is specified, the gapped lines will be plotted in order on this axes. If None, the current axes (plt.gca()) is used.\n",
" line_color=\"black\", # The color of the gapped lines.\n",
Expand All @@ -136,11 +136,10 @@
"):\n",
" \"\"\"\n",
" Function to plot the standard deviations as vertical errorbars.\n",
" For proportion and Sankey plots, the vertical bars instead show the\n",
" BSE of the proportion.\n",
" The mean is a gap defined by negative space.\n",
"\n",
" This function combines the functionality of gapped_lines(),\n",
" proportional_error_bar(), and sankey_error_bar().\n",
"\n",
" \"\"\"\n",
"\n",
" if gap_width_percent < 0 or gap_width_percent > 100:\n",
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10 changes: 7 additions & 3 deletions nbs/tutorials/04-proportion_plot.ipynb
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Expand Up @@ -646,7 +646,7 @@
"id": "243a1a0b",
"metadata": {},
"source": [
"Instead of a Gardner-Altman plot, you can generate a **Cumming estimation plot** by setting ``float_contrast=False`` in the ``.plot()`` method. This will plot the bootstrap effect sizes below the raw data."
"Instead of a Gardner-Altman plot, you can generate a **Cumming estimation plot** by setting ``float_contrast=False`` in the ``.plot()`` method. This will plot the bootstrap effect sizes below the raw data. The gapped lines show the mean (gap) and the binomial standard error (BSE) of each group."
]
},
{
Expand Down Expand Up @@ -1098,7 +1098,7 @@
"id": "17832542",
"metadata": {},
"source": [
"The Sankey plots for paired proportions also supports the ``float_contrast`` parameter, which can be set to ``False`` to produce a **Cumming estimation plot**.\n"
"The Sankey plots for paired proportions also supports the ``float_contrast`` parameter, which can be set to ``False`` to produce a **Cumming estimation plot**. The gapped lines show the mean and the BSE of each group.\n"
]
},
{
Expand Down Expand Up @@ -1687,7 +1687,11 @@
}
],
"source": [
"two_groups_unpaired.mean_diff.plot(barplot_kwargs={\"alpha\":0.5, \"edgecolor\":\"red\", \"linewidth\":2, 'errorbar': ('sd', 0.1)});"
"# Note on error bars for proportion plots: you can pass a seaborn `errorbar`\n",
"# argument through barplot_kwargs, such as 'errorbar': ('sd', 1) for the standard\n",
"# deviation. DABEST's proportion plots instead show the BSE,\n",
"# √(p(1-p)/n).\n",
"two_groups_unpaired.mean_diff.plot(barplot_kwargs={\"alpha\":0.5, \"edgecolor\":\"red\", \"linewidth\":2});"
]
},
{
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2 changes: 1 addition & 1 deletion nbs/tutorials/08-plot_aesthetics.ipynb
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Expand Up @@ -1299,7 +1299,7 @@
"source": [
"The type of group summary can be specified via `group_summaries` in the `.plot()` method and must be one of these: `'median_quartiles'`, `'mean_sd'`, `None`.\n",
"\n",
"By default, the group summary is set to `'mean_sd'`."
"By default, the group summary is set to `'mean_sd'`. For proportion and Sankey plots, the `'mean_sd'` gapped line shows the BSE, not the standard deviation."
]
},
{
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