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merged 4 commits into from
Feb 19, 2025
Merged

delta delta and mini meta aesthetic changes #200

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fa9c2d8
Add gap to contrast axes zeroline for delta-delta experiments and fix…
JAnns98 Feb 18, 2025
8c75b03
Edited delta-delta and mini-meta (non horizontal) layouts
JAnns98 Feb 19, 2025
3dacd32
Edit horizontal plot mini-meta and delta-delta
JAnns98 Feb 19, 2025
5ecac36
removed old commented out code
JAnns98 Feb 19, 2025
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54 changes: 34 additions & 20 deletions dabest/misc_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -734,7 +734,7 @@ def initialize_fig(
all_groups_count = np.sum([len(i) for i in dabest_obj.idx])
# Increase the width (vertical layout) or height (horizontal layout) for delta-delta or mini-meta graph
if show_delta2 or show_mini_meta:
all_groups_count += 2
all_groups_count += 1

if horizontal:
frac = 0.3 if is_paired or show_mini_meta else 0.5
Expand Down Expand Up @@ -1217,7 +1217,7 @@ def set_xaxis_ticks_and_lims(
contrast_axes.set_xticks(rawdata_axes.get_xticks())
else:
temp = rawdata_axes.get_xticks()
temp = np.append(temp, [max(temp) + 1, max(temp) + 2])
temp = np.append(temp, [max(temp) + 1])
contrast_axes.set_xticks(temp)

# Lims
Expand All @@ -1227,13 +1227,21 @@ def set_xaxis_ticks_and_lims(

if float_contrast:
contrast_axes.set_xlim(0.5, 1.5)
elif show_delta2 or show_mini_meta:

if show_delta2:
if show_pairs:
rawdata_axes.set_xlim(-0.375, 4.75)
else:
rawdata_axes.set_xlim(-0.5, 4.75)
contrast_axes.set_xlim(rawdata_axes.get_xlim())

elif show_mini_meta:
# Increase the xlim of raw data by 2
temp = rawdata_axes.get_xlim()
if show_pairs:
rawdata_axes.set_xlim(temp[0], temp[1] + 0.5)
else:
rawdata_axes.set_xlim(temp[0], temp[1] + 2)
rawdata_axes.set_xlim(temp[0], temp[1] + 1)
contrast_axes.set_xlim(rawdata_axes.get_xlim())
else:
contrast_axes.set_xlim(rawdata_axes.get_xlim())
Expand Down Expand Up @@ -1529,19 +1537,33 @@ def gardner_altman_adjustments(
def draw_zeroline(
ax : axes.Axes,
horizontal : bool,
reflines_kwargs : dict
reflines_kwargs : dict,
extra_delta : bool,
):
# If 0 lies within the ylim of the contrast axes, draw a zero reference line.
ax_lim = ax.get_xlim() if horizontal else ax.get_ylim()
method = ax.axvline if horizontal else ax.axhline
if extra_delta and not horizontal:
contrast_xlim = [-0.5, 3.4]
delta2_xlim = [3.6, 4.75]

if ax.get_ylim()[0] < ax.get_ylim()[1]:
contrast_lim_low, contrast_lim_high = ax.get_ylim()
else:
contrast_lim_high, contrast_lim_low = ax.get_ylim()

if ax_lim[0] < ax_lim[1]:
contrast_lim_low, contrast_lim_high = ax_lim
if contrast_lim_low < 0 < contrast_lim_high:
ax.hlines(y=0, xmin=contrast_xlim[0], xmax=contrast_xlim[1], **reflines_kwargs)
ax.hlines(y=0, xmin=delta2_xlim[0], xmax=delta2_xlim[1], **reflines_kwargs)
else:
contrast_lim_high, contrast_lim_low = ax_lim
ax_lim = ax.get_xlim() if horizontal else ax.get_ylim()
method = ax.axvline if horizontal else ax.axhline

if ax_lim[0] < ax_lim[1]:
contrast_lim_low, contrast_lim_high = ax_lim
else:
contrast_lim_high, contrast_lim_low = ax_lim

if contrast_lim_low < 0 < contrast_lim_high:
method(0, **reflines_kwargs)
if contrast_lim_low < 0 < contrast_lim_high:
method(0, **reflines_kwargs)

def redraw_independent_spines(
rawdata_axes : axes.Axes,
Expand Down Expand Up @@ -1616,14 +1638,6 @@ def redraw_independent_spines(
ax.set_xlim(xlim)
ax.set_ylim(ylim)
del redraw_axes_kwargs["y"]

# Add x-spine line for delta2/mini meta.
if extra_delta:
ylim = contrast_axes.get_ylim()
redraw_axes_kwargs["y"] = ylim[0]
x_ticks = contrast_axes.get_xticks()
contrast_axes.hlines(xmin=x_ticks[-2], xmax=x_ticks[-1], **redraw_axes_kwargs)
del redraw_axes_kwargs["y"]

def redraw_dependent_spines(
rawdata_axes: axes.Axes,
Expand Down
152 changes: 111 additions & 41 deletions dabest/plot_tools.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -1042,7 +1042,7 @@ def swarm_contrast_bar_plotter(
if horizontal:
ax_to_plot.add_patch(mpatches.Rectangle((0, max(axes[0].get_yticks())-0.5), diff, 0.5, color='black', **bar_kwargs))
else:
ax_to_plot.add_patch(mpatches.Rectangle((max(axes[0].get_xticks())+2-0.25, 0), 0.5, diff, color='black', **bar_kwargs))
ax_to_plot.add_patch(mpatches.Rectangle((max(axes[0].get_xticks())+1-0.25, 0), 0.5, diff, color='black', **bar_kwargs))

ax_to_plot.set_xlim(og_xlim)
ax_to_plot.set_ylim(og_ylim)
Expand Down Expand Up @@ -1144,8 +1144,8 @@ def delta_text_plotter(
X_Adjust = 0.48 if delta_text_x_location == 'right' else -0.38
X_Adjust += delta_text_x_adjustment
delta_text_x_coordinates = [x+X_Adjust for x in delta_text_x_coordinates]
if show_mini_meta: delta_text_x_coordinates.append(max(swarm_plot_ax.get_xticks())+2+X_Adjust)
if show_delta2: delta_text_x_coordinates.append(max(swarm_plot_ax.get_xticks())+2-0.35)
if show_mini_meta: delta_text_x_coordinates.append(max(swarm_plot_ax.get_xticks())+1+X_Adjust)
if show_delta2: delta_text_x_coordinates.append(max(swarm_plot_ax.get_xticks())+1+X_Adjust)
if show_mini_meta or show_delta2: ticks_to_plot.append(max(ticks_to_plot)+1)

# Collect the Y-coordinates for the delta text
Expand Down Expand Up @@ -1390,6 +1390,7 @@ def plot_minimeta_or_deltadelta_violins(
show_delta2: bool,
plot_kwargs: dict,
horizontal: bool,
show_pairs: bool,
es_marker_kwargs: dict,
es_errorbar_kwargs: dict
):
Expand Down Expand Up @@ -1424,6 +1425,8 @@ def plot_minimeta_or_deltadelta_violins(
Keyword arguments for the plot.
horizontal : bool
If the plot is horizontal.
show_pairs : bool
Whether the data is paired and shown in pairs.
es_marker_kwargs: dict
Keyword arguments for the effectsize marker.
es_errorbar_kwargs: dict
Expand All @@ -1445,12 +1448,12 @@ def extract_curve_data(dabest_object):

if horizontal:
violinplot_kwargs.update({'vert': False, 'widths': 1})
position = max(rawdata_axes.get_yticks()) + 2
position = max(rawdata_axes.get_yticks()) + 1
half = "bottom"
effsize_x, effsize_y = difference, [position]
ci_x, ci_y = [ci_low, ci_high], [position, position]
else:
position = max(rawdata_axes.get_xticks()) + 2
position = max(rawdata_axes.get_xticks()) + 1
half = "right"
effsize_x, effsize_y = [position], difference
ci_x, ci_y = [position, position], [ci_low, ci_high]
Expand Down Expand Up @@ -1489,18 +1492,21 @@ def extract_curve_data(dabest_object):

else:
if show_mini_meta:
contrast_xtick_labels.extend(["", "Weighted Delta"])
if show_pairs:
contrast_xtick_labels.extend(["Weighted\n Delta"])
else:
contrast_xtick_labels.extend(["Weighted Delta"])
elif effect_size == "hedges_g":
contrast_xtick_labels.extend(["", "Deltas' g"])
contrast_xtick_labels.extend(["Deltas' g"])
else:
contrast_xtick_labels.extend(["", "Delta-Delta"])
contrast_xtick_labels.extend(["Delta-Delta"])

# Create the delta-delta axes.
if show_delta2 and not horizontal:
if plot_kwargs["delta2_label"] is not None:
delta2_label = plot_kwargs["delta2_label"]
elif effect_size == "mean_diff":
delta2_label = "Delta - Delta"
delta2_label = "Delta-Delta"
else:
delta2_label = "Deltas' g"
fontsize_delta2label = plot_kwargs["fontsize_delta2label"]
Expand Down Expand Up @@ -1874,29 +1880,51 @@ def gridkey_plotter(
# Add delta-delta or mini_meta details to the table
if show_mini_meta or show_delta2:
if show_delta2:
added_group_name = ["deltas' g"] if effect_size == "hedges_g" else ["delta-delta"]
added_group_name = ["Deltas' g"] if effect_size == "hedges_g" else ["Delta-Delta"]
else:
added_group_name = ["Weighted delta"]
added_group_name = ["Weighted Delta"]
gridkey_rows = added_group_name + gridkey_rows
table_cellcols = [[""]*len(table_cellcols[0])] + table_cellcols

for group_idx, group_vals in enumerate(table_cellcols):
if group_idx == 0:
added_group = ['', gridkey_marker]
elif gridkey_show_es and (group_idx == len(table_cellcols)-1) and not horizontal:
added_delta_effectsize = delta_delta.difference if show_delta2 else mini_meta.difference
added_delta_effectsize_str = np.format_float_positional(
added_delta_effectsize,
precision=2,
sign=True,
trim="k",
min_digits=2,
)
added_group = ['-', added_delta_effectsize_str]
else:
added_group = ['', '']
for n in added_group:
group_vals.append(n)
if not horizontal and show_delta2:
extra_table_cellcols = [[] for i in range(len(table_cellcols))]

for group_idx, group_vals in enumerate(extra_table_cellcols):
if group_idx == 0:
added_group = [gridkey_marker]
elif gridkey_show_es and (group_idx == len(extra_table_cellcols)-1) and not horizontal:
added_delta_effectsize = delta_delta.difference
added_delta_effectsize_str = np.format_float_positional(
added_delta_effectsize,
precision=2,
sign=True,
trim="k",
min_digits=2,
)
added_group = [added_delta_effectsize_str]
else:
added_group = ['']
for n in added_group:
group_vals.append(n)

elif horizontal or show_mini_meta:
for group_idx, group_vals in enumerate(table_cellcols):
if group_idx == 0:
added_group = [gridkey_marker]
elif gridkey_show_es and (group_idx == len(table_cellcols)-1) and not horizontal:
added_delta_effectsize = delta_delta.difference if show_delta2 else mini_meta.difference
added_delta_effectsize_str = np.format_float_positional(
added_delta_effectsize,
precision=2,
sign=True,
trim="k",
min_digits=2,
)
added_group = [added_delta_effectsize_str]
else:
added_group = ['']
for n in added_group:
group_vals.append(n)

# Create the table object
if horizontal:
Expand Down Expand Up @@ -1936,18 +1964,60 @@ def gridkey_plotter(
)
else:
# Plot the table for vertical format
gridkey = ax_to_plot.table(
cellText=table_cellcols,
rowLabels=gridkey_rows,
cellLoc="center",
bbox=[
0,
-len(gridkey_rows) * 0.1 - 0.05,
1,
len(gridkey_rows) * 0.1,
],
**{"alpha": 0.5}
)
if show_mini_meta:
gridkey = ax_to_plot.table(
cellText=table_cellcols,
rowLabels=gridkey_rows,
cellLoc="center",
bbox=[
0,
-len(gridkey_rows) * 0.1 - 0.05,
1,
len(gridkey_rows) * 0.1,
],
**{"alpha": 0.5}
)

elif show_delta2:
gridkey = ax_to_plot.table(
cellText=table_cellcols,
rowLabels=gridkey_rows,
cellLoc="center",
bbox=[
0,
-len(gridkey_rows) * 0.1 - 0.05,
0.75,
len(gridkey_rows) * 0.1,
],
**{"alpha": 0.5}
)

extra_gridkey = ax_to_plot.table(
cellText=extra_table_cellcols,
cellLoc="center",
bbox=[
0.78,
-len(gridkey_rows) * 0.1 - 0.05,
0.15,
len(gridkey_rows) * 0.1,
],
**{"alpha": 0.5}
)

else:
gridkey = ax_to_plot.table(
cellText=table_cellcols,
rowLabels=gridkey_rows,
cellLoc="center",
bbox=[
0,
-len(gridkey_rows) * 0.1 - 0.05,
1,
len(gridkey_rows) * 0.1,
],
**{"alpha": 0.5}
)

# modifies row label cells
for cell in gridkey._cells:
if cell[1] == -1:
Expand Down Expand Up @@ -2133,7 +2203,7 @@ def table_for_horizontal_plots(

### Plot the text
if show_mini_meta or show_delta2:
new_ticks = ticks_to_plot + [max(ticks_to_plot)+2]
new_ticks = ticks_to_plot + [max(ticks_to_plot)+1]
else:
new_ticks = ticks_to_plot.copy()
for i,loc in zip(tab.index, new_ticks):
Expand Down
6 changes: 3 additions & 3 deletions dabest/plotter.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -391,10 +391,10 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
show_delta2 = show_delta2,
plot_kwargs = plot_kwargs,
horizontal = horizontal,
show_pairs = show_pairs,
es_marker_kwargs = es_marker_kwargs,
es_errorbar_kwargs = es_errorbar_kwargs
)

## Contrast bars
contrast_bars = plot_kwargs["contrast_bars"]
if contrast_bars:
Expand Down Expand Up @@ -452,7 +452,6 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
proportional = proportional,
horizontal = horizontal,
)

# Plot aesthetic adjustments.
if float_contrast: # For Gardner-Altman (float contrast) plots only.
gardner_altman_adjustments(
Expand All @@ -476,7 +475,8 @@ def effectsize_df_plotter(effectsize_df: object, **plot_kwargs) -> matplotlib.fi
draw_zeroline(
ax = contrast_axes,
horizontal = horizontal,
reflines_kwargs = reflines_kwargs
reflines_kwargs = reflines_kwargs,
extra_delta = True if show_delta2 else False,
)
## Axes independent spine lines
is_gridkey = True if plot_kwargs["gridkey_rows"] is not None else False
Expand Down
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