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Credited help from GitHub user for jitter and edits to adjust table d…
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…elta values location and general plotter trimming
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@JAnns98
JAnns98 committed Oct 9, 2024
1 parent 1c639f1 commit eae1792
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Showing 7 changed files with 191 additions and 146 deletions.
2 changes: 2 additions & 0 deletions dabest/_modidx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,8 @@
'dabest/misc_tools.py'),
'dabest.misc_tools.extract_contrast_plotting_ticks': ( 'API/misc_tools.html#extract_contrast_plotting_ticks',
'dabest/misc_tools.py'),
'dabest.misc_tools.extract_group_summaries': ( 'API/misc_tools.html#extract_group_summaries',
'dabest/misc_tools.py'),
'dabest.misc_tools.get_color_palette': ('API/misc_tools.html#get_color_palette', 'dabest/misc_tools.py'),
'dabest.misc_tools.get_kwargs': ('API/misc_tools.html#get_kwargs', 'dabest/misc_tools.py'),
'dabest.misc_tools.get_params': ('API/misc_tools.html#get_params', 'dabest/misc_tools.py'),
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67 changes: 63 additions & 4 deletions dabest/misc_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
__all__ = ['merge_two_dicts', 'unpack_and_add', 'print_greeting', 'get_varname', 'get_unique_categories', 'get_params',
'get_kwargs', 'get_color_palette', 'initialize_fig', 'get_plot_groups', 'add_counts_to_ticks',
'extract_contrast_plotting_ticks', 'set_xaxis_ticks_and_lims', 'show_legend',
'Gardner_Altman_Plot_Aesthetic_Adjustments', 'Cumming_Plot_Aesthetic_Adjustments', 'Redraw_Spines']
'Gardner_Altman_Plot_Aesthetic_Adjustments', 'Cumming_Plot_Aesthetic_Adjustments', 'Redraw_Spines',
'extract_group_summaries']

# %% ../nbs/API/misc_tools.ipynb 4
import datetime as dt
Expand Down Expand Up @@ -103,7 +104,6 @@ def get_params(effectsize_df, plot_kwargs):
plot_kwargs : dict
Kwargs passed to the plot function.
"""
dabest_obj = effectsize_df.dabest_obj
plot_data = effectsize_df._plot_data
xvar = effectsize_df.xvar
yvar = effectsize_df.yvar
Expand All @@ -112,8 +112,11 @@ def get_params(effectsize_df, plot_kwargs):
mini_meta = effectsize_df.mini_meta
effect_size = effectsize_df.effect_size
proportional = effectsize_df.proportional
results = effectsize_df.results
dabest_obj = effectsize_df.dabest_obj
all_plot_groups = dabest_obj._all_plot_groups
idx = dabest_obj.idx


if effect_size not in ["mean_diff", "delta_g"] or not delta2:
show_delta2 = False
Expand Down Expand Up @@ -159,9 +162,15 @@ def get_params(effectsize_df, plot_kwargs):
horizontal = plot_kwargs["horizontal"]
if horizontal:
float_contrast = False

# Contrast Axes kwargs
es_marker_size = plot_kwargs["es_marker_size"]
halfviolin_alpha = plot_kwargs["halfviolin_alpha"]
ci_type = plot_kwargs["ci_type"]

return (dabest_obj, plot_data, xvar, yvar, is_paired, effect_size, proportional, all_plot_groups, idx,
show_delta2, show_mini_meta, float_contrast, show_pairs, effect_size_type, group_summaries, err_color, horizontal)
show_delta2, show_mini_meta, float_contrast, show_pairs, effect_size_type, group_summaries, err_color, horizontal,
results, es_marker_size, halfviolin_alpha, ci_type)

def get_kwargs(plot_kwargs, ytick_color):
"""
Expand Down Expand Up @@ -1328,7 +1337,6 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
A boolean flag to determine if the plot is for horizontal plotting.
"""


# If 0 lies within the ylim of the contrast axes, draw a zero reference line.
if horizontal:
contrast_axes_lim = contrast_axes.get_xlim()
Expand Down Expand Up @@ -1488,3 +1496,54 @@ def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contras
for ax, xlim, ylim in zip([rawdata_axes, contrast_axes], [og_xlim_raw, og_xlim_contrast], [og_ylim_raw, og_ylim_contrast]):
ax.set_xlim(xlim)
ax.set_ylim(ylim)


def extract_group_summaries(proportional, err_color, rawdata_axes, asymmetric_side, horizontal,
bootstraps_color_by_group, plot_palette_raw, all_plot_groups,
n_groups, color_col, ytick_color, plot_kwargs):

from .plot_tools import get_swarm_spans

if proportional:
group_summaries_method = "proportional_error_bar"
group_summaries_offset = 0
group_summaries_line_color = err_color
else:
# Create list to gather xspans.
xspans = []
line_colors = []
for jj, c in enumerate(rawdata_axes.collections):
try:
if asymmetric_side == "right":
# currently offset is hardcoded with value of -0.2
x_max_span = -0.2
else:
if horizontal:
x_max_span = 0.1 # currently offset is hardcoded with value of 0.1
else:
_, x_max, _, _ = get_swarm_spans(c)
x_max_span = x_max - jj
xspans.append(x_max_span)
except TypeError:
# we have got a None, so skip and move on.
pass

if bootstraps_color_by_group:
line_colors.append(plot_palette_raw[all_plot_groups[jj]])

# Break the loop since hue in Seaborn adds collections to axes and it will result in index out of range
if jj >= n_groups - 1 and color_col is None:
break

if len(line_colors) != len(all_plot_groups):
line_colors = ytick_color

# hue in swarmplot would add collections to axes which will result in len(xspans) = len(all_plot_groups) + len(unique groups in hue)
if len(xspans) > len(all_plot_groups):
xspans = xspans[:len(all_plot_groups)]

group_summaries_method = "gapped_lines"
group_summaries_offset = xspans + np.array(plot_kwargs["group_summaries_offset"])
group_summaries_line_color = line_colors

return group_summaries_method, group_summaries_offset, group_summaries_line_color
10 changes: 4 additions & 6 deletions dabest/plot_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1282,7 +1282,8 @@ def slopegraph_plotter(dabest_obj, plot_data, xvar, yvar, color_col, plot_palett
horizontal : bool
If the plotting will be in horizontal format.
"""
# Jitter Kwargs
# Jitter Kwargs
# With help from devMJBL
jitter = slopegraph_kwargs["jitter"]
if jitter >= 1:
err0 = "Jitter value is too high. Defaulting to 1."
Expand Down Expand Up @@ -1313,10 +1314,7 @@ def slopegraph_plotter(dabest_obj, plot_data, xvar, yvar, color_col, plot_palett
grp_count = len(current_tuple)
# Iterate through the data for the current tuple.
for ID, observation in current_pair.iterrows():
# x_points = [t for t in range(x_start, x_start + grp_count)]
# y_points = observation[yvar].tolist()

x_points = [t + 0.15*jitter*rng.standard_t(df=6, size=None) for t in range(x_start, x_start + grp_count)]
x_points = [t + 0.15*jitter*rng.standard_t(df=6, size=None) for t in range(x_start, x_start + grp_count)] # devMJBL
y_points = observation[yvar].tolist()

if color_col is None:
Expand Down Expand Up @@ -1814,7 +1812,7 @@ def table_for_horizontal_plots(effectsize_df, ax, contrast_axes, ticks_to_plot,
table_font_size = table_kwargs['fontsize'] if table_kwargs['text_units'] == None else table_kwargs['fontsize']-2
table_text_color = table_kwargs['text_color']
text_units = '' if table_kwargs['text_units'] == None else table_kwargs['text_units']
table_gap_dashes = table_kwargs['paired_gap_dashes']
table_gap_dashes = table_kwargs['paired_gap_dashes'] # Currently unused
fontsize_label = table_kwargs['fontsize_label']
label = table_kwargs['label']

Expand Down
91 changes: 28 additions & 63 deletions dabest/plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,6 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
contrast_bars=True, contrast_bars_kwargs=None,
delta_text=True, delta_text_kwargs=None,
delta_dot=True, delta_dot_kwargs=None,
horizontal=False, horizontal_table_kwargs=None,
"""
from .misc_tools import (
Expand All @@ -77,9 +76,9 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
Gardner_Altman_Plot_Aesthetic_Adjustments,
Cumming_Plot_Aesthetic_Adjustments,
Redraw_Spines,
extract_group_summaries
)
from .plot_tools import (
get_swarm_spans,
error_bar,
sankeydiag,
swarmplot,
Expand Down Expand Up @@ -114,11 +113,12 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
ytick_color = plt.rcParams["ytick.color"]

# Extract parameters and set kwargs
(dabest_obj, plot_data, xvar, yvar, is_paired, effect_size, proportional,
all_plot_groups, idx, show_delta2, show_mini_meta, float_contrast,
show_pairs, effect_size_type, group_summaries, err_color, horizontal) = get_params(
(dabest_obj, plot_data, xvar, yvar, is_paired, effect_size,
proportional, all_plot_groups, idx, show_delta2, show_mini_meta,
float_contrast, show_pairs, effect_size_type, group_summaries,
err_color, horizontal, results, es_marker_size, halfviolin_alpha, ci_type) = get_params(
effectsize_df=effectsize_df,
plot_kwargs=plot_kwargs
plot_kwargs=plot_kwargs,
)

(swarmplot_kwargs, barplot_kwargs, sankey_kwargs, violinplot_kwargs, slopegraph_kwargs,
Expand Down Expand Up @@ -279,48 +279,21 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):

# Plot the error bars.
if group_summaries is not None:
if proportional:
group_summaries_method = "proportional_error_bar"
group_summaries_offset = 0
group_summaries_line_color = err_color
else:
# Create list to gather xspans.
xspans = []
line_colors = []
for jj, c in enumerate(rawdata_axes.collections):
try:
if asymmetric_side == "right":
# currently offset is hardcoded with value of -0.2
x_max_span = -0.2
else:
if horizontal:
x_max_span = 0.1 # currently offset is hardcoded with value of 0.1
else:
_, x_max, _, _ = get_swarm_spans(c)
x_max_span = x_max - jj
xspans.append(x_max_span)
except TypeError:
# we have got a None, so skip and move on.
pass

if bootstraps_color_by_group:
line_colors.append(plot_palette_raw[all_plot_groups[jj]])

# Break the loop since hue in Seaborn adds collections to axes and it will result in index out of range
if jj >= n_groups - 1 and color_col is None:
break

if len(line_colors) != len(all_plot_groups):
line_colors = ytick_color

# hue in swarmplot would add collections to axes which will result in len(xspans) = len(all_plot_groups) + len(unique groups in hue)
if len(xspans) > len(all_plot_groups):
xspans = xspans[:len(all_plot_groups)]

group_summaries_method = "gapped_lines"
group_summaries_offset = xspans + np.array(plot_kwargs["group_summaries_offset"])
group_summaries_line_color = line_colors

(group_summaries_method,
group_summaries_offset, group_summaries_line_color) = extract_group_summaries(
proportional=proportional,
err_color=err_color,
rawdata_axes=rawdata_axes,
asymmetric_side=asymmetric_side if not proportional else None,
horizontal=horizontal,
bootstraps_color_by_group=bootstraps_color_by_group,
plot_palette_raw=plot_palette_raw,
all_plot_groups=all_plot_groups,
n_groups=n_groups,
color_col=color_col,
ytick_color=ytick_color,
plot_kwargs=plot_kwargs
)
# Plot
error_bar(
plot_data,
Expand All @@ -337,7 +310,6 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
)

# Add the counts to the rawdata axes xticks.
# if not horizontal:
add_counts_to_ticks(
plot_data=plot_data,
xvar=xvar,
Expand All @@ -347,12 +319,11 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
horizontal=horizontal,
)

# Enforce the xtick of rawdata_axes to be 0 and 1 after drawing only one sankey ----> Redundant code
# if one_sankey:
# rawdata_axes.set_xticks([0, 1])

# Plot effect sizes and bootstraps.
plot_groups = temp_all_plot_groups if (is_paired == "baseline" and show_pairs and two_col_sankey) else temp_idx if (two_col_sankey) else all_plot_groups
plot_groups = (temp_all_plot_groups if (is_paired == "baseline" and show_pairs and two_col_sankey)
else temp_idx if two_col_sankey
else all_plot_groups
)

(ticks_to_skip, ticks_to_plot,
ticks_to_skip_contrast, ticks_to_start_twocol_sankey) = extract_contrast_plotting_ticks(
Expand All @@ -365,15 +336,11 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
)

# Adjust contrast tick locations to account for different plotting styles in horizontal plots
table_axes_ticks_to_plot = ticks_to_plot
if (horizontal and proportional and not show_pairs) or (horizontal and plot_kwargs["swarm_side"] == "right"):
ticks_to_plot = [x+0.25 for x in ticks_to_plot]

# Plot the bootstraps, then the effect sizes and CIs.
es_marker_size = plot_kwargs["es_marker_size"]
halfviolin_alpha = plot_kwargs["halfviolin_alpha"]
ci_type = plot_kwargs["ci_type"]
results = effectsize_df.results

(current_group, current_control,
current_effsize, contrast_xtick_labels) = effect_size_curve_plotter(
ticks_to_plot=ticks_to_plot,
Expand Down Expand Up @@ -463,7 +430,6 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
reflines_kwargs=reflines_kwargs,
redraw_axes_kwargs=redraw_axes_kwargs,
)

else:
# For Cumming Plots only.
Cumming_Plot_Aesthetic_Adjustments(
Expand Down Expand Up @@ -494,8 +460,7 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
horizontal=horizontal
)


################################################### GRIDKEY WIP
# GRIDKEY WIP
# if gridkey_rows is None, skip everything here
gridkey_rows = plot_kwargs["gridkey_rows"]
if gridkey_rows is not None and not horizontal:
Expand Down Expand Up @@ -592,7 +557,7 @@ def effectsize_df_plotter(effectsize_df, **plot_kwargs):
effectsize_df=effectsize_df,
ax = table_axes,
contrast_axes=contrast_axes,
ticks_to_plot=ticks_to_plot,
ticks_to_plot=table_axes_ticks_to_plot,
show_mini_meta=show_mini_meta,
show_delta2=show_delta2,
table_kwargs=table_kwargs,
Expand Down
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