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Merge pull request #193 from ACCLAB/feat-horizontal-plots
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Added Horizontal plots and various additional features, documentation, tutorial, tests, and improving code clarity
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@Jacobluke-
Jacobluke- authored Dec 23, 2024
2 parents 3de867f + aa61ed2 commit 5658cd0
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1 change: 1 addition & 0 deletions README.md
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# DABEST-Python


<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

[![minimal Python
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4 changes: 2 additions & 2 deletions dabest/_dabest_object.py
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Expand Up @@ -5,15 +5,15 @@
# %% auto 0
__all__ = ['Dabest']

# %% ../nbs/API/dabest_object.ipynb 4
# %% ../nbs/API/dabest_object.ipynb 5
# Import standard data science libraries
from numpy import array, repeat, random, issubdtype, number
import numpy as np
import pandas as pd
from scipy.stats import norm
from scipy.stats import randint

# %% ../nbs/API/dabest_object.ipynb 6
# %% ../nbs/API/dabest_object.ipynb 7
class Dabest(object):

"""
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108 changes: 75 additions & 33 deletions dabest/_effsize_objects.py
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Expand Up @@ -358,12 +358,6 @@ def _perform_statistical_test(self):
# References:
# https://en.wikipedia.org/wiki/McNemar%27s_test

# df_temp = pd.DataFrame({"control": self.__control, "test": self.__test})
# x1 = len(df_temp[(df_temp["control"] == 0) & (df_temp["test"] == 0)])
# x2 = len(df_temp[(df_temp["control"] == 0) & (df_temp["test"] == 1)])
# x3 = len(df_temp[(df_temp["control"] == 1) & (df_temp["test"] == 0)])
# x4 = len(df_temp[(df_temp["control"] == 1) & (df_temp["test"] == 1)])
# table = [[x1, x2], [x3, x4]]
x1 = np.sum((self.__control == 0) & (self.__test == 0))
x2 = np.sum((self.__control == 0) & (self.__test == 1))
x3 = np.sum((self.__control == 1) & (self.__test == 0))
Expand Down Expand Up @@ -1146,21 +1140,16 @@ def plot(
show_delta2=True,
show_mini_meta=True,
group_summaries=None,
group_summaries_offset=0.1,
fig_size=None,
dpi=100,
ax=None,
gridkey_rows=None,
gridkey_merge_pairs=False,
gridkey_show_Ns=True,
gridkey_show_es=True,
swarmplot_kwargs=None,
barplot_kwargs=None,
violinplot_kwargs=None,
slopegraph_kwargs=None,
sankey_kwargs=None,
reflines_kwargs=None,
group_summary_kwargs=None,
group_summaries_kwargs=None,
legend_kwargs=None,
title=None,
fontsize_title=16,
Expand All @@ -1169,7 +1158,7 @@ def plot(
fontsize_contrastxlabel=12,
fontsize_contrastylabel=12,
fontsize_delta2label=12,
#### Contrast bars and delta text and delta dots WIP ####
#### Contrast bars, Swarm bars, delta text, and delta dots WIP ####
contrast_bars=True,
swarm_bars=True,
contrast_bars_kwargs=None,
Expand All @@ -1180,7 +1169,30 @@ def plot(
delta_text_kwargs=None,
delta_dot=True,
delta_dot_kwargs=None,
show_baseline_ec=False,

# Horizontal Plots
horizontal=False,
horizontal_table_kwargs=None,

# Gridkey
gridkey_rows=None,
gridkey_merge_pairs=False,
gridkey_show_Ns=True,
gridkey_show_es=True,
gridkey_delimiters=[';', '>', '_'],
gridkey_kwargs=None,

es_marker_kwargs=None,
es_errorbar_kwargs=None,

prop_sample_counts=False,
prop_sample_counts_kwargs=None,

es_paired_lines=True,
es_paired_lines_kwargs=None,

# Basline EffectSize Curve
show_baseline_ec=False,
):
"""
Creates an estimation plot for the effect size of interest.
Expand Down Expand Up @@ -1259,24 +1271,20 @@ def plot(
notched line beside each group. If 'median_quantiles', then the
median and 25th and 75th percentiles of each group is plotted
instead. If 'None', the summaries are not shown.
group_summaries_offset : float, default 0.1
If group summaries are displayed, they will be offset from the raw
data swarmplot groups by this value.
fig_size : tuple, default None
The desired dimensions of the figure as a (length, width) tuple.
dpi : int, default 100
The dots per inch of the resulting figure.
ax : matplotlib.Axes, default None
Provide an existing Axes for the plots to be created. If no Axes is
specified, a new matplotlib Figure will be created.
gridkey_rows : list, default None
Provide a list of row labels for the gridkey. The supplied idx is
checked against the row labels to determine whether the corresponding
cell should be populated or not.
swarmplot_kwargs : dict, default None
Pass any keyword arguments accepted by the seaborn `swarmplot`
command here, as a dict. If None, the following keywords are
passed to sns.swarmplot : {'size':`raw_marker_size`}.
barplot_kwargs : dict, default None
By default, the keyword arguments passed are:
{"estimator": np.mean, "errorbar": plot_kwargs["ci"]}
violinplot_kwargs : dict, default None
Pass any keyword arguments accepted by the matplotlib `
pyplot.violinplot` command here, as a dict. If None, the following
Expand All @@ -1287,7 +1295,7 @@ def plot(
of observations when `show_pairs=True`. Pass any keyword arguments
accepted by matplotlib `plot()` function here, as a dict.
If None, the following keywords are
passed to plot() : {'linewidth':1, 'alpha':0.5}.
passed to plot() : {'linewidth':1, 'alpha':0.5, 'jitter':0, 'jitter_seed':9876543210}.
sankey_kwargs: dict, default None
Whis will change the appearance of the sankey diagram used to depict
paired proportional data when `show_pairs=True` and `proportional=True`.
Expand All @@ -1300,12 +1308,13 @@ def plot(
command here, as a dict. If None, the following keywords are
passed to Axes.hlines : {'linestyle':'solid', 'linewidth':0.75,
'zorder':2, 'color' : default y-tick color}.
group_summary_kwargs : dict, default None
group_summaries_kwargs : dict, default None
Pass any keyword arguments accepted by the matplotlib.lines.Line2D
command here, as a dict. This will change the appearance of the
vertical summary lines for each group, if `group_summaries` is not
'None'. If None, the following keywords are passed to
matplotlib.lines.Line2D : {'lw':2, 'alpha':1, 'zorder':3}.
matplotlib.lines.Line2D : {'lw':2, 'alpha':1, 'zorder':3,
'gap_width_percent':1.5, 'offset':0.1, 'color':None}.
legend_kwargs : dict, default None
Pass any keyword arguments accepted by the matplotlib Axes
`legend` command here, as a dict. If None, the following keywords
Expand All @@ -1330,39 +1339,73 @@ def plot(
fontsize_delta2label : float, default 12
Font size for the delta-delta axes ylabel.
contrast_bars : boolean, default True
Whether or not to display the contrast bars.
swarm_bars : boolean, default True
Whether or not to display the swarm bars.
contrast_bars_kwargs : dict, default None
Pass relevant keyword arguments to the contrast bars. Pass any keyword arguments accepted by
matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
{"color": None, "alpha": 0.3}
{"color": None, "zorder":-3}
swarm_bars_kwargs : dict, default None
Pass relevant keyword arguments to the swarm bars. Pass any keyword arguments accepted by
matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
{"color": None, "alpha": 0.3}
{"color": None, "zorder":-3}
summary_bars : list, default None
Pass a list of indices of the contrast objects to have summary bars displayed on the plot.
For example, [0,1] will show summary bars for the first two contrast objects.
summary_bars_kwargs: dict, default None
If None, the following keywords are passed: {"color": None, "alpha": 0.15}
If None, the following keywords are passed: {"span_ax": False, "color": None, "alpha": 0.15, "zorder":-3}
delta_text : boolean, default True
Whether or not to display the text deltas.
delta_text_kwargs : dict, default None
Pass relevant keyword arguments to the delta text. Pass any keyword arguments accepted by
matplotlib.text.Text here, as a string. If None, the following keywords are passed:
{"color": None, "alpha": 1, "fontsize": 10, "ha": 'center', "va": 'center', "rotation": 0,
"x_location": 'right', "x_coordinates": None, "y_coordinates": None}
Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
"x_location": 'right', "x_coordinates": None, "y_coordinates": None, "offset": 0}
Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
Use "x_adjust" to adjust the x location of all the texts (positive moves right, negative left).
delta_dot : boolean, default True
Whether or not to display the delta dots on paired or repeated measure plots.
delta_dot_kwargs : dict, default None
Pass relevant keyword arguments. If None, the following keywords are passed:
{"marker": "^", "alpha": 0.5, "zorder": 2, "size": 3, "side": "right"}
show_baseline_ec : boolean, default False
{"color": 'k', "marker": "^", "alpha": 0.5, "zorder": -1, "size": 3, "side": "right"}
horizontal_table_kwargs : dict, default None
{'show: True, 'color' : 'yellow', 'alpha' :0.2, 'fontsize' : 12, 'text_color' : 'black',
'text_units' : None, 'control_marker' : '-', 'fontsize_label': 12, 'label': 'Δ'}
gridkey_rows : list, default None
cell should be populated or not.
Pass relevant keyword arguments to the gridkey. If None, the following keywords are passed:
{ 'show_es' : True, # If True, the gridkey will show the effect size of each comparison.
'show_Ns' :True, # If True, the gridkey will show the number of observations in eachgroup.
'merge_pairs' : False, # If True, the gridkey will merge the pairs of groups into a single cell. This is useful for when the groups are paired.
'delimiters': [';', '>', '_'], # Delimiters to split the group names.
'marker': "\u25CF", # Marker for the gridkey dots.
}
es_marker_kwargs: dict, default None
Pass relevant keyword arguments to the effectsize marker plotting. If none, the following keywords are passed:
{'marker': 'o', 'size': plot_kwargs['es_marker_size'], 'color': 'black', 'alpha': 1, 'zorder': 1}
es_errorbar_kwargs: dict, default None
Pass relevant keyword arguments to the effectsize errorbar plotting. If none, the following keywords are passed:
{'color': 'black', 'lw': 2, 'linestyle': '-', 'alpha': 1,'zorder': 1,}
prop_sample_counts: bool, default False
Show the sample counts for each group in proportional plots
prop_sample_counts_kwargs: dict, default None
Pass relevant keyword arguments. If None, the following keywords are passed:
{'color': 'k', 'zorder': 5, 'ha': 'center', 'va': 'center'},
es_paired_lines: bool, default True
Whether or not to add lines to connect the effect size curves in paired plots.
es_paired_lines_kwargs: dict, default None
Pass relevant plot keyword arguments. If None, the following keywords are passed:
{"linestyle": "-", "linewidth": 2, "zorder": -2, "color": 'dimgray', "alpha": 1}
show_baseline_ec : boolean, default False
Whether or not to display the baseline error curve. The baseline error curve
represents the distribution of the effect size when comparing the control
group to itself, providing a reference for the inherent variability or noise
Expand Down Expand Up @@ -1402,7 +1445,6 @@ def plot(
del all_kwargs["self"]

out = effectsize_df_plotter(self, **all_kwargs)

return out

@property
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11 changes: 8 additions & 3 deletions dabest/_modidx.py
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Expand Up @@ -81,12 +81,13 @@
'dabest/misc_tools.py'),
'dabest.misc_tools.Gardner_Altman_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#gardner_altman_plot_aesthetic_adjustments',
'dabest/misc_tools.py'),
'dabest.misc_tools.General_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#general_plot_aesthetic_adjustments',
'dabest/misc_tools.py'),
'dabest.misc_tools.Redraw_Spines': ('API/misc_tools.html#redraw_spines', 'dabest/misc_tools.py'),
'dabest.misc_tools.add_counts_to_ticks': ( 'API/misc_tools.html#add_counts_to_ticks',
'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'),
Expand Down Expand Up @@ -115,6 +116,8 @@
'dabest/plot_tools.py'),
'dabest.plot_tools.SwarmPlot._swarm': ('API/plot_tools.html#swarmplot._swarm', 'dabest/plot_tools.py'),
'dabest.plot_tools.SwarmPlot.plot': ('API/plot_tools.html#swarmplot.plot', 'dabest/plot_tools.py'),
'dabest.plot_tools.add_counts_to_prop_plots': ( 'API/plot_tools.html#add_counts_to_prop_plots',
'dabest/plot_tools.py'),
'dabest.plot_tools.barplotter': ('API/plot_tools.html#barplotter', 'dabest/plot_tools.py'),
'dabest.plot_tools.check_data_matches_labels': ( 'API/plot_tools.html#check_data_matches_labels',
'dabest/plot_tools.py'),
Expand All @@ -126,7 +129,7 @@
'dabest/plot_tools.py'),
'dabest.plot_tools.error_bar': ('API/plot_tools.html#error_bar', 'dabest/plot_tools.py'),
'dabest.plot_tools.get_swarm_spans': ('API/plot_tools.html#get_swarm_spans', 'dabest/plot_tools.py'),
'dabest.plot_tools.grid_key_WIP': ('API/plot_tools.html#grid_key_wip', 'dabest/plot_tools.py'),
'dabest.plot_tools.gridkey_plotter': ('API/plot_tools.html#gridkey_plotter', 'dabest/plot_tools.py'),
'dabest.plot_tools.halfviolin': ('API/plot_tools.html#halfviolin', 'dabest/plot_tools.py'),
'dabest.plot_tools.normalize_dict': ('API/plot_tools.html#normalize_dict', 'dabest/plot_tools.py'),
'dabest.plot_tools.plot_minimeta_or_deltadelta_violins': ( 'API/plot_tools.html#plot_minimeta_or_deltadelta_violins',
Expand All @@ -140,5 +143,7 @@
'dabest.plot_tools.swarm_bars_plotter': ( 'API/plot_tools.html#swarm_bars_plotter',
'dabest/plot_tools.py'),
'dabest.plot_tools.swarmplot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
'dabest.plot_tools.table_for_horizontal_plots': ( 'API/plot_tools.html#table_for_horizontal_plots',
'dabest/plot_tools.py'),
'dabest.plot_tools.width_determine': ('API/plot_tools.html#width_determine', 'dabest/plot_tools.py')},
'dabest.plotter': {'dabest.plotter.effectsize_df_plotter': ('API/plotter.html#effectsize_df_plotter', 'dabest/plotter.py')}}}
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