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Merged
merged 3 commits into from
Aug 25, 2025
Merged

Updated slopegraph visuals and additional custom_palette options #208

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fd1b16c
Updated slopegraph format to include group summaries
JAnns98 Aug 18, 2025
905a4ad
Add custom_palette option for coloring barplots with 0 and 1 keys
JAnns98 Aug 21, 2025
ef4d4b5
Updated edge thickness for barplots with the custom palette [0,1] dic…
JAnns98 Aug 22, 2025
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5 changes: 3 additions & 2 deletions dabest/_effsize_objects.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -1143,7 +1143,7 @@ def plot(
face_color=None,

raw_desat=0.5, # swarm_desat=0.5, OLD # bar_desat=0.5, OLD
contrast_desat=1, # halfviolin_desat=1, OLD
contrast_desat=1.0, # halfviolin_desat=1, OLD

raw_alpha=None, # NEW
contrast_alpha=0.8, # halfviolin_alpha=0.8, OLD
Expand Down Expand Up @@ -1478,7 +1478,8 @@ def plot(

if raw_alpha is None:
raw_alpha = (0.4 if self.is_proportional and self.is_paired
else 0.5 if self.is_paired
else 0.5 if self.is_paired and (color_col is not None or self.__delta2)
else 0.2 if self.is_paired and color_col is None
else 1.0
)

Expand Down
45 changes: 35 additions & 10 deletions dabest/misc_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,8 @@ def get_params(

def get_kwargs(
plot_kwargs: dict,
ytick_color
ytick_color,
is_paired: bool = False
):
"""
Extracts the kwargs from the `plot_kwargs` object for use in the plotter function.
Expand All @@ -214,6 +215,8 @@ def get_kwargs(
Kwargs passed to the plot function.
ytick_color : str or color list
Color of the yticks.
is_paired : bool, optional
A boolean flag to determine if the plot is for paired data. Default is False.
"""
from .misc_tools import merge_two_dicts

Expand Down Expand Up @@ -334,7 +337,7 @@ def get_kwargs(
default_group_summaries_kwargs = {
"zorder": 3,
"lw": 2,
"alpha": 1,
"alpha": 1 if not is_paired else 0.6,
'gap_width_percent': 1.5,
'offset': 0.1,
'color': None
Expand Down Expand Up @@ -513,7 +516,7 @@ def get_color_palette(
idx: list,
all_plot_groups: list,
delta2: bool,
sankey: bool
proportional: bool
):
"""
Create the color palette to be used in the plotter function.
Expand All @@ -534,9 +537,11 @@ def get_color_palette(
A list of all the group names.
delta2 : bool
A boolean flag to determine if the plot will have a delta-delta effect size.
sankey : bool
A boolean flag to determine if the plot is for a Sankey diagram.
proportional : bool
A boolean flag to determine if the plot is for a proportional plot.
"""
sankey = True if proportional and show_pairs else False

# Create color palette that will be shared across subplots.
color_col = plot_kwargs["color_col"]
if color_col is None:
Expand All @@ -548,7 +553,13 @@ def get_color_palette(
color_groups = pd.unique(plot_data[color_col])
bootstraps_color_by_group = False
if show_pairs:
bootstraps_color_by_group = False
if plot_kwargs["custom_palette"] is not None:
if delta2 or sankey:
bootstraps_color_by_group = False
else:
bootstraps_color_by_group = True
else:
bootstraps_color_by_group = False

# Handle the color palette.
filled = True
Expand Down Expand Up @@ -599,6 +610,17 @@ def get_color_palette(
groups_in_palette = {
k: custom_pal[k] for k in color_groups
}
elif proportional and not sankey: # barplots (unpaired proportional data)
keys = list(custom_pal.keys())
if all(k in keys for k in [1, 0]) and len(keys) == 2:
groups_in_palette = {
k: custom_pal[k] for k in [1, 0]
}
bootstraps_color_by_group = False
else:
groups_in_palette = {
k: custom_pal[k] for k in all_plot_groups if k in color_groups
}
elif sankey:
groups_in_palette = {
k: custom_pal[k] for k in [1, 0]
Expand Down Expand Up @@ -1856,13 +1878,15 @@ def color_picker(color_type: str,
elements: list,
color_col: str,
show_pairs: bool,
color_palette: dict) -> list:
color_palette: dict,
bootstraps_color_by_group: bool) -> list:
num_of_elements = len(elements)
colors = (
[kwargs.pop('color')] * num_of_elements
if kwargs.get('color', None) is not None
else ['black'] * num_of_elements
if color_col is not None or show_pairs
# if color_col is not None or show_pairs
if color_col is not None or not bootstraps_color_by_group
else list(color_palette.values())
)
if color_type in ['contrast', 'summary', 'delta_text']:
Expand All @@ -1877,7 +1901,7 @@ def color_picker(color_type: str,
return final_colors


def prepare_bars_for_plot(bar_type, bar_kwargs, horizontal, plot_palette_raw, color_col, show_pairs,
def prepare_bars_for_plot(bar_type, bar_kwargs, horizontal, plot_palette_raw, color_col, show_pairs, bootstraps_color_by_group,
plot_data = None, xvar = None, yvar = None, # Raw data
results = None, ticks_to_plot = None, extra_delta = None, # Contrast data
reference_band = None, summary_axes = None, ci_type = None # Summary data
Expand Down Expand Up @@ -1951,7 +1975,8 @@ def prepare_bars_for_plot(bar_type, bar_kwargs, horizontal, plot_palette_raw, co
elements = ticks_to_plot if bar_type=='contrast' else ticks,
color_col = color_col,
show_pairs = show_pairs,
color_palette = plot_palette_raw
color_palette = plot_palette_raw,
bootstraps_color_by_group = bootstraps_color_by_group
)
if bar_type == 'contrast' and extra_delta is not None:
colors.append('black')
Expand Down
67 changes: 61 additions & 6 deletions dabest/plot_tools.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -904,6 +904,7 @@ def delta_text_plotter(
show_pairs: bool,
float_contrast: bool,
extra_delta: float,
bootstraps_color_by_group: bool = False
):
"""
Add delta text to the contrast plot.
Expand All @@ -928,6 +929,8 @@ def delta_text_plotter(
Whether the DABEST plot uses Gardner-Altman or Cummings.
extra_delta : float or None
The extra mini-meta or delta-delta value if applicable.
bootstraps_color_by_group : bool, optional
Whether to color the bootstraps by group. Default is False.
"""
# Colors
from .misc_tools import color_picker
Expand All @@ -936,7 +939,8 @@ def delta_text_plotter(
elements = ticks_to_plot,
color_col = color_col,
show_pairs = show_pairs,
color_palette = plot_palette_raw
color_palette = plot_palette_raw,
bootstraps_color_by_group = bootstraps_color_by_group
)

num_of_elements = len(ticks_to_plot) + 1 if extra_delta is not None else len(ticks_to_plot)
Expand Down Expand Up @@ -1091,7 +1095,8 @@ def slopegraph_plotter(
temp_idx: list,
horizontal: bool,
temp_all_plot_groups: list,
plot_kwargs: dict
plot_kwargs: dict,
group_summaries_kwargs: dict
):
"""
Add slopegraph to the rawdata axes.
Expand Down Expand Up @@ -1124,6 +1129,8 @@ def slopegraph_plotter(
List of all plot groups.
plot_kwargs : dict
Keyword arguments for the plot.
group_summaries_kwargs : dict, optional
Keyword arguments for group summaries, if applicable.

"""
# Jitter Kwargs
Expand Down Expand Up @@ -1178,6 +1185,45 @@ def slopegraph_plotter(
x_points, y_points = (y_points, x_points) if horizontal else (x_points, y_points)
rawdata_axes.plot(x_points, y_points, **slopegraph_kwargs)

# Add the group summaries if applicable.
group_summaries = plot_kwargs.get("group_summaries", None)
if group_summaries is not None:
for key in ['gap_width_percent', 'offset']:
group_summaries_kwargs.pop(key, None)
group_summaries_kwargs['color'] = 'black' if group_summaries_kwargs.get('color') is None else group_summaries_kwargs['color']
group_summaries_kwargs['capsize'] = 0 if group_summaries_kwargs.get('capsize') is None else group_summaries_kwargs['capsize']

index_points = [t for t in range(x_start, x_start + grp_count)]
av_points, err_points, lo_points, hi_points = [], [], [], []
for group in range(len(index_points)):
if group_summaries == "mean_sd":
av_points.append(current_pair.iloc[:, int(group)].mean())
err_points.append(current_pair.iloc[:, int(group)].std())
elif group_summaries == "median_quartiles":
median = current_pair.iloc[:, int(group)].median()
av_points.append(median)
lo_points.append(median - current_pair.iloc[:, int(group)].quantile(0.25))
hi_points.append(current_pair.iloc[:, int(group)].quantile(0.75) - median)

if group_summaries == "median_quartiles":
err_points = [lo_points, hi_points]

# Plot the lines
if horizontal:
rawdata_axes.errorbar(
av_points,
index_points,
xerr=err_points,
**group_summaries_kwargs
)
else:
rawdata_axes.errorbar(
index_points,
av_points,
yerr=err_points,
**group_summaries_kwargs
)

x_start = x_start + grp_count

# Set the tick labels, because the slopegraph plotting doesn't.
Expand Down Expand Up @@ -1839,6 +1885,9 @@ def barplotter(
horizontal : bool
If the plot is horizontal.
"""
# Check if the custom_palette is a dictionary with two keys 0 and 1 (for filled bar coloring)
filled_bars = True if len(plot_palette_raw.keys())==2 and all(k in plot_palette_raw for k in [1, 0]) else False

bar_width = barplot_kwargs.get('width', 0.5)
fontsize = barplot_kwargs.pop('fontsize')

Expand Down Expand Up @@ -1866,29 +1915,35 @@ def barplotter(
for hue_val in bar1_df[color_col]
]
else:
edge_colors = raw_colors
edge_colors = len(all_plot_groups)*['black',] if filled_bars else raw_colors

bar1 = sns.barplot(
data=bar1_df,
x=xvar,
y="proportion",
ax=rawdata_axes,
order=all_plot_groups,
linewidth=2,
facecolor=(1, 1, 1, 0),
linewidth=1 if filled_bars else 2,
facecolor=plot_palette_raw[0] if filled_bars else (1, 1, 1, 0),
edgecolor=edge_colors,
zorder=1,
orient=orient,
)

if filled_bars:
barplot_kwargs['facecolor'] = plot_palette_raw[1]
barplot_kwargs['edgecolor'] = 'black'
barplot_kwargs['linewidth'] = 1
else:
barplot_kwargs['palette'] = plot_palette_raw

bar2 = sns.barplot(
data=plot_data,
x=yvar if horizontal else xvar,
y=xvar if horizontal else yvar,
hue=xvar if color_col is None else color_col,
ax=rawdata_axes,
order=all_plot_groups,
palette=plot_palette_raw,
dodge=False,
zorder=1,
orient=orient,
Expand Down
14 changes: 10 additions & 4 deletions dabest/plotter.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,8 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
raw_bars_kwargs, contrast_bars_kwargs, table_kwargs, gridkey_kwargs, contrast_marker_kwargs,
contrast_errorbar_kwargs, prop_sample_counts_kwargs, contrast_paired_lines_kwargs) = get_kwargs(
plot_kwargs = plot_kwargs,
ytick_color = ytick_color
ytick_color = ytick_color,
is_paired = effectsize_df.is_paired
)

(dabest_obj, plot_data, xvar, yvar, is_paired, effect_size, proportional,
Expand All @@ -160,7 +161,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
idx = idx,
all_plot_groups = all_plot_groups,
delta2 = effectsize_df.delta2,
sankey = True if proportional and show_pairs else False,
proportional = proportional
)

# Initialise the figure.
Expand Down Expand Up @@ -219,6 +220,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
horizontal = horizontal,
temp_all_plot_groups = temp_all_plot_groups,
plot_kwargs = plot_kwargs,
group_summaries_kwargs = group_summaries_kwargs
)

## Add delta dots to the contrast axes for paired plots.
Expand Down Expand Up @@ -333,7 +335,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi

## Swarm bars
raw_bars = plot_kwargs["raw_bars"]
if raw_bars and not proportional and not horizontal: #Currently not supporting swarm bars for horizontal plots (looks weird)
if raw_bars and not proportional and not is_paired and not horizontal: #Currently not supporting swarm bars for horizontal plots (looks weird)
raw_bars_dict, raw_bars_kwargs = prepare_bars_for_plot(
bar_type = 'raw',
bar_kwargs = raw_bars_kwargs,
Expand All @@ -343,7 +345,8 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
show_pairs = show_pairs,
plot_data = plot_data,
xvar = xvar,
yvar = yvar,
yvar = yvar,
bootstraps_color_by_group = bootstraps_color_by_group,
)
add_bars_to_plot(bar_dict = raw_bars_dict,
ax = rawdata_axes,
Expand Down Expand Up @@ -424,6 +427,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
show_pairs = show_pairs,
results = results,
ticks_to_plot = ticks_to_plot,
bootstraps_color_by_group = bootstraps_color_by_group,
extra_delta = (effectsize_df.mini_meta.difference if show_mini_meta
else effectsize_df.delta_delta.difference if show_delta2
else None)
Expand All @@ -445,6 +449,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
plot_palette_raw = plot_palette_raw,
show_pairs = show_pairs,
float_contrast = float_contrast,
bootstraps_color_by_group = bootstraps_color_by_group,
extra_delta = (effectsize_df.mini_meta.difference if show_mini_meta
else effectsize_df.delta_delta.difference if show_delta2
else None),
Expand Down Expand Up @@ -588,6 +593,7 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
reference_band = reference_band,
summary_axes = contrast_axes,
ci_type = ci_type,
bootstraps_color_by_group = bootstraps_color_by_group,
)

add_bars_to_plot(bar_dict = reference_band_dict,
Expand Down
5 changes: 3 additions & 2 deletions nbs/API/effsize_objects.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1343,7 +1343,7 @@
" face_color=None,\n",
"\n",
" raw_desat=0.5, # swarm_desat=0.5, OLD # bar_desat=0.5, OLD\n",
" contrast_desat=1, # halfviolin_desat=1, OLD\n",
" contrast_desat=1.0, # halfviolin_desat=1, OLD\n",
"\n",
" raw_alpha=None, # NEW\n",
" contrast_alpha=0.8, # halfviolin_alpha=0.8, OLD\n",
Expand Down Expand Up @@ -1678,7 +1678,8 @@
"\n",
" if raw_alpha is None:\n",
" raw_alpha = (0.4 if self.is_proportional and self.is_paired \n",
" else 0.5 if self.is_paired\n",
" else 0.5 if self.is_paired and (color_col is not None or self.__delta2)\n",
" else 0.2 if self.is_paired and color_col is None\n",
" else 1.0\n",
" )\n",
"\n",
Expand Down
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