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Merge branch 'vnbdev' of github.com:ACCLAB/DABEST-python into pullrequests/siemdejong/issue-183
# Conflicts: # dabest/_modidx.py # dabest/misc_tools.py # dabest/plot_tools.py # dabest/plotter.py # nbs/API/misc_tools.ipynb # nbs/API/plot_tools.ipynb # nbs/API/plotter.ipynb
2 parents 9a42975 + 360fdc3 commit 3ac4852

134 files changed

Lines changed: 5724 additions & 3806 deletions

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‎.gitignore‎

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@@ -5,6 +5,7 @@ _proc/
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.gitattributes
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.last_checked
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.gitconfig
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.cursorignore
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*.bak
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*.log
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*~

‎README.md‎

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<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
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[![minimal Python
6-
version](https://img.shields.io/badge/Python%3E%3D-3.8-6666ff.svg)](https://www.anaconda.com/distribution/)
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version](https://img.shields.io/badge/Python%3E%3D-3.9-6666ff.svg)](https://www.anaconda.com/distribution/)
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[![PyPI
88
version](https://badge.fury.io/py/dabest.svg)](https://badge.fury.io/py/dabest)
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[![Downloads](https://img.shields.io/pepy/dt/dabest.svg)](https://pepy.tech/project/dabest)

‎dabest/_dabest_object.py‎

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# %% ../nbs/API/dabest_object.ipynb 4
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# Import standard data science libraries
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from numpy import array, repeat, random, issubdtype, number
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import numpy as np
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import pandas as pd
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from scipy.stats import norm
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from scipy.stats import randint
@@ -479,7 +480,7 @@ def _check_errors(self, x, y, idx, experiment, experiment_label, x1_level):
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# Handling str type condition
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if is_str_condition_met:
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if len(pd.unique(idx).tolist()) != 2:
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if len(np.unique(idx).tolist()) != 2:
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err0 = "`mini_meta` is True, but `idx` ({})".format(idx)
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err1 = "does not contain exactly 2 unique columns."
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raise ValueError(err0 + err1)

‎dabest/_effsize_objects.py‎

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@@ -973,6 +973,7 @@ def plot(
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contrast_ylim=None,
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delta2_ylim=None,
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swarm_side=None,
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empty_circle=False,
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custom_palette=None,
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swarm_desat=0.5,
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halfviolin_desat=1,
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fig_size=None,
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dpi=100,
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ax=None,
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contrast_show_es=False,
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es_sf=2,
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es_fontsize=10,
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contrast_show_deltas=True,
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gridkey_rows=None,
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gridkey_merge_pairs=False,
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gridkey_show_Ns=True,
@@ -1019,6 +1016,17 @@ def plot(
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fontsize_contrastxlabel=12,
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fontsize_contrastylabel=12,
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fontsize_delta2label=12,
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#### Contrast bars and delta text and delta dots WIP ####
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contrast_bars=True,
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swarm_bars=True,
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contrast_bars_kwargs=None,
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swarm_bars_kwargs=None,
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summary_bars=None,
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summary_bars_kwargs=None,
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delta_text=True,
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delta_text_kwargs=None,
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delta_dot=True,
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delta_dot_kwargs=None,
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):
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"""
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Creates an estimation plot for the effect size of interest.
@@ -1066,6 +1074,12 @@ def plot(
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https://seaborn.pydata.org/generated/seaborn.cubehelix_palette.html
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The named colors of matplotlib can be found here:
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https://matplotlib.org/examples/color/named_colors.html
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swarm_side: string, default None
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The side on which points are swarmed for swarmplots ("center", "left", or "right").
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empty_circle: boolean, default False
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Boolean value determining if empty circles will be used for plotting of
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swarmplot for control groups. Color of each individual swarm is also now
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dependent on the comparison group.
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swarm_desat : float, default 1
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Decreases the saturation of the colors in the swarmplot by the
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desired proportion. Uses `seaborn.desaturate()` to acheive this.
@@ -1161,7 +1175,39 @@ def plot(
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Font size for the contrast axes ylabel.
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fontsize_delta2label : float, default 12
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Font size for the delta-delta axes ylabel.
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contrast_bars : boolean, default True
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Whether or not to display the contrast bars.
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swarm_bars : boolean, default True
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Whether or not to display the swarm bars.
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contrast_bars_kwargs : dict, default None
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Pass relevant keyword arguments to the contrast bars. Pass any keyword arguments accepted by
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matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
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{"color": None, "alpha": 0.3}
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swarm_bars_kwargs : dict, default None
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Pass relevant keyword arguments to the swarm bars. Pass any keyword arguments accepted by
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matplotlib.patches.Rectangle here, as a string. If None, the following keywords are passed:
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{"color": None, "alpha": 0.3}
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1193+
summary_bars : list, default None
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Pass a list of indices of the contrast objects to have summary bars displayed on the plot.
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For example, [0,1] will show summary bars for the first two contrast objects.
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summary_bars_kwargs: dict, default None
1197+
If None, the following keywords are passed: {"color": None, "alpha": 0.15}
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delta_text : boolean, default True
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Whether or not to display the text deltas.
1200+
delta_text_kwargs : dict, default None
1201+
Pass relevant keyword arguments to the delta text. Pass any keyword arguments accepted by
1202+
matplotlib.text.Text here, as a string. If None, the following keywords are passed:
1203+
{"color": None, "alpha": 1, "fontsize": 10, "ha": 'center', "va": 'center', "rotation": 0,
1204+
"x_location": 'right', "x_coordinates": None, "y_coordinates": None}
1205+
Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
1206+
delta_dot : boolean, default True
1207+
Whether or not to display the delta dots on paired or repeated measure plots.
1208+
delta_dot_kwargs : dict, default None
1209+
Pass relevant keyword arguments. If None, the following keywords are passed:
1210+
{"marker": "^", "alpha": 0.5, "zorder": 2, "size": 3, "side": "right"}
11651211
11661212
Returns
11671213
-------
@@ -1182,7 +1228,7 @@ def plot(
11821228
if hasattr(self, "results") is False:
11831229
self.__pre_calc()
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1185-
if self.__delta2:
1231+
if self.__delta2 and not empty_circle:
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color_col = self.__x2
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11881234
# if self.__proportional:

‎dabest/_modidx.py‎

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@@ -64,14 +64,35 @@
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'dabest.forest_plot': { 'dabest.forest_plot.extract_plot_data': ( 'API/forest_plot.html#extract_plot_data',
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'dabest/forest_plot.py'),
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'dabest.forest_plot.forest_plot': ('API/forest_plot.html#forest_plot', 'dabest/forest_plot.py'),
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'dabest.forest_plot.load_plot_data': ('API/forest_plot.html#load_plot_data', 'dabest/forest_plot.py')},
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'dabest.misc_tools': { 'dabest.misc_tools.get_unique_categories': ( 'API/misc_tools.html#get_unique_categories',
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'dabest.forest_plot.load_plot_data': ('API/forest_plot.html#load_plot_data', 'dabest/forest_plot.py'),
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'dabest.forest_plot.map_effect_attribute': ( 'API/forest_plot.html#map_effect_attribute',
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'dabest/forest_plot.py')},
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'dabest.misc_tools': { 'dabest.misc_tools.Cumming_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#cumming_plot_aesthetic_adjustments',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.Gardner_Altman_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#gardner_altman_plot_aesthetic_adjustments',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.General_Plot_Aesthetic_Adjustments': ( 'API/misc_tools.html#general_plot_aesthetic_adjustments',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.add_counts_to_ticks': ( 'API/misc_tools.html#add_counts_to_ticks',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.extract_contrast_plotting_ticks': ( 'API/misc_tools.html#extract_contrast_plotting_ticks',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.get_color_palette': ('API/misc_tools.html#get_color_palette', 'dabest/misc_tools.py'),
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'dabest.misc_tools.get_kwargs': ('API/misc_tools.html#get_kwargs', 'dabest/misc_tools.py'),
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'dabest.misc_tools.get_params': ('API/misc_tools.html#get_params', 'dabest/misc_tools.py'),
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'dabest.misc_tools.get_plot_groups': ('API/misc_tools.html#get_plot_groups', 'dabest/misc_tools.py'),
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'dabest.misc_tools.get_unique_categories': ( 'API/misc_tools.html#get_unique_categories',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.get_varname': ('API/misc_tools.html#get_varname', 'dabest/misc_tools.py'),
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'dabest.misc_tools.initialize_fig': ('API/misc_tools.html#initialize_fig', 'dabest/misc_tools.py'),
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'dabest.misc_tools.merge_two_dicts': ('API/misc_tools.html#merge_two_dicts', 'dabest/misc_tools.py'),
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'dabest.misc_tools.print_greeting': ('API/misc_tools.html#print_greeting', 'dabest/misc_tools.py'),
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'dabest.misc_tools.set_xaxis_ticks_and_lims': ( 'API/misc_tools.html#set_xaxis_ticks_and_lims',
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'dabest/misc_tools.py'),
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'dabest.misc_tools.show_legend': ('API/misc_tools.html#show_legend', 'dabest/misc_tools.py'),
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'dabest.misc_tools.unpack_and_add': ('API/misc_tools.html#unpack_and_add', 'dabest/misc_tools.py')},
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'dabest.plot_tools': { 'dabest.plot_tools.SwarmPlot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
94+
'dabest.plot_tools': { 'dabest.plot_tools.DeltaDotsPlotter': ('API/plot_tools.html#deltadotsplotter', 'dabest/plot_tools.py'),
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'dabest.plot_tools.SwarmPlot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
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'dabest.plot_tools.SwarmPlot.__init__': ( 'API/plot_tools.html#swarmplot.__init__',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.SwarmPlot._adjust_gutter_points': ( 'API/plot_tools.html#swarmplot._adjust_gutter_points',
@@ -84,14 +105,30 @@
84105
'dabest/plot_tools.py'),
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'dabest.plot_tools.SwarmPlot._swarm': ('API/plot_tools.html#swarmplot._swarm', 'dabest/plot_tools.py'),
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'dabest.plot_tools.SwarmPlot.plot': ('API/plot_tools.html#swarmplot.plot', 'dabest/plot_tools.py'),
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'dabest.plot_tools.barplotter': ('API/plot_tools.html#barplotter', 'dabest/plot_tools.py'),
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'dabest.plot_tools.check_data_matches_labels': ( 'API/plot_tools.html#check_data_matches_labels',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.contrast_bars_plotter': ( 'API/plot_tools.html#contrast_bars_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.delta_text_plotter': ( 'API/plot_tools.html#delta_text_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.effect_size_curve_plotter': ( 'API/plot_tools.html#effect_size_curve_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.error_bar': ('API/plot_tools.html#error_bar', 'dabest/plot_tools.py'),
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'dabest.plot_tools.get_swarm_spans': ('API/plot_tools.html#get_swarm_spans', 'dabest/plot_tools.py'),
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'dabest.plot_tools.grid_key_WIP': ('API/plot_tools.html#grid_key_wip', 'dabest/plot_tools.py'),
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'dabest.plot_tools.halfviolin': ('API/plot_tools.html#halfviolin', 'dabest/plot_tools.py'),
92121
'dabest.plot_tools.normalize_dict': ('API/plot_tools.html#normalize_dict', 'dabest/plot_tools.py'),
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'dabest.plot_tools.plot_minimeta_or_deltadelta_violins': ( 'API/plot_tools.html#plot_minimeta_or_deltadelta_violins',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.sankeydiag': ('API/plot_tools.html#sankeydiag', 'dabest/plot_tools.py'),
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'dabest.plot_tools.single_sankey': ('API/plot_tools.html#single_sankey', 'dabest/plot_tools.py'),
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'dabest.plot_tools.slopegraph_plotter': ( 'API/plot_tools.html#slopegraph_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.summary_bars_plotter': ( 'API/plot_tools.html#summary_bars_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.swarm_bars_plotter': ( 'API/plot_tools.html#swarm_bars_plotter',
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'dabest/plot_tools.py'),
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'dabest.plot_tools.swarmplot': ('API/plot_tools.html#swarmplot', 'dabest/plot_tools.py'),
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'dabest.plot_tools.width_determine': ('API/plot_tools.html#width_determine', 'dabest/plot_tools.py')},
97134
'dabest.plotter': {'dabest.plotter.effectsize_df_plotter': ('API/plotter.html#effectsize_df_plotter', 'dabest/plotter.py')}}}

‎dabest/_stats_tools/effsize.py‎

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@@ -223,7 +223,7 @@ def cohens_h(control:list|tuple|np.ndarray,
223223
)->float:
224224
'''
225225
Computes Cohen's h for test v.s. control.
226-
See [here](https://en.wikipedia.org/wiki/Cohen%27s_h for reference.)
226+
See [here](https://en.wikipedia.org/wiki/Cohen%27s_h) for reference.
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228228
`Notes`:
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