Implement HorizontalEffectPlot
This commit is contained in:
parent
138e31751a
commit
71b714ab7d
GPG Key ID:
7234E476BF21C61A
|
|
@ -18,7 +18,7 @@ from .bayes_factors import bayesfactor_afbf
|
|||
from .config import config
|
||||
from .descriptives import auto_correlations, auto_descriptives
|
||||
from .distributions import beta_oddsratio, beta_ratio, hdi, transformed_dist
|
||||
from .graphs import init_fonts
|
||||
from .graphs import init_fonts, HorizontalEffectPlot
|
||||
from .io import pickle_read_compressed, pickle_read_encrypted, pickle_write_compressed, pickle_write_encrypted
|
||||
from .regress import IntervalCensoredCox, Logit, OLS, OrdinalLogit, PenalisedLogit, Poisson, regress, vif
|
||||
from .sig_tests import anova_oneway, auto_univariable, chi2, mannwhitney, pearsonr, spearman, ttest_ind, ttest_ind_multiple
|
||||
|
|
|
|||
161
yli/graphs.py
161
yli/graphs.py
|
|
@ -1,3 +1,21 @@
|
|||
# scipy-yli: Helpful SciPy utilities and recipes
|
||||
# Copyright © 2022–2023 Lee Yingtong Li (RunasSudo)
|
||||
#
|
||||
# This program is free software: you can redistribute it and/or modify
|
||||
# it under the terms of the GNU Affero General Public License as published by
|
||||
# the Free Software Foundation, either version 3 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful,
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
# GNU Affero General Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU Affero General Public License
|
||||
# along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
|
||||
from collections import namedtuple
|
||||
|
||||
def init_fonts():
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
|
|
@ -5,3 +23,146 @@ def init_fonts():
|
|||
plt.rcParams['text.latex.preamble'] = r'\usepackage{tgheros}\usepackage{newtxmath}'
|
||||
plt.rcParams['font.size'] = 11
|
||||
plt.rcParams['figure.dpi'] = 100
|
||||
|
||||
EffectPlotData = namedtuple('EffectPlotData', ['y', 'mean', 'ci0', 'ci1', 'pvalue'])
|
||||
|
||||
class EffectPlotText:
|
||||
def __init__(self, y, text, skip_width=False, **kwargs):
|
||||
self.y = y
|
||||
self.text = text
|
||||
self.skip_width = skip_width
|
||||
self.kwargs = kwargs
|
||||
|
||||
class HorizontalEffectPlot:
|
||||
# TODO: Documentation
|
||||
|
||||
def __init__(self, measure_name, xlabel, *, header_y=1):
|
||||
self.measure_name = measure_name
|
||||
self.xlabel = xlabel
|
||||
|
||||
self.text_left = [[]] # [EffectPlotText]
|
||||
#self.text_right = [[], [], [], [], [], [], []] # [EffectPlotText]
|
||||
self.text_right = [[], [], [], [], [], []] # [EffectPlotText]
|
||||
self.data = []
|
||||
|
||||
#self.space_right = [0.15, 0.05, 0, 0, 0.1, 0, 0] # Space in inches between each right text column
|
||||
self.space_right = [0.15, 0.05, 0, 0, 0.1, 0] # Space in inches between each right text column
|
||||
|
||||
# Add headings
|
||||
self.text_right[0].append(EffectPlotText(header_y, measure_name, skip_width=True, ha='center', fontweight='medium'))
|
||||
self.text_right[2].append(EffectPlotText(header_y, '(95% CI)', skip_width=True, ha='center', fontweight='medium'))
|
||||
self.text_right[5].append(EffectPlotText(header_y, 'p', skip_width=True, ha='center', fontweight='medium', fontstyle='italic'))
|
||||
|
||||
def add_nobar(self, y, label, mean=None, ci0=None, ci1=None, pvalue=None):
|
||||
# Label
|
||||
self.text_left[0].append(EffectPlotText(y, label, ha='right'))
|
||||
|
||||
# Mean
|
||||
if mean is not None:
|
||||
self.text_right[0].append(EffectPlotText(y, mean, ha='right'))
|
||||
|
||||
# Confidence intervals
|
||||
if ci0 is not None:
|
||||
self.text_right[1].append(EffectPlotText(y, '({}'.format(ci0), ha='right'))
|
||||
self.text_right[2].append(EffectPlotText(y, '–', ha='left'))
|
||||
self.text_right[3].append(EffectPlotText(y, '{})'.format(ci1), ha='left'))
|
||||
|
||||
# P value and flag
|
||||
if pvalue is not None:
|
||||
self.text_right[5].append(EffectPlotText(y, pvalue, ha='right'))
|
||||
|
||||
def add_bar(self, y, label, mean, ci0, ci1, pvalue):
|
||||
self.data.append(EffectPlotData(y=y, mean=mean, ci0=ci0, ci1=ci1, pvalue=pvalue))
|
||||
|
||||
# Label
|
||||
self.text_left[0].append(EffectPlotText(y, label, ha='right'))
|
||||
|
||||
# Mean
|
||||
self.text_right[0].append(EffectPlotText(y, '{:.2f}'.format(mean), ha='right'))
|
||||
|
||||
# Confidence intervals
|
||||
self.text_right[1].append(EffectPlotText(y, '({:.2f}'.format(ci0), ha='right'))
|
||||
self.text_right[2].append(EffectPlotText(y, '–', ha='left'))
|
||||
self.text_right[3].append(EffectPlotText(y, '{:.2f})'.format(ci1), ha='left'))
|
||||
|
||||
# P value and flag
|
||||
if pvalue < 0.0005:
|
||||
self.text_right[4].append(EffectPlotText(y, '<', ha='left'))
|
||||
self.text_right[5].append(EffectPlotText(y, '0.001*', ha='left'))
|
||||
elif pvalue < 0.01:
|
||||
self.text_right[5].append(EffectPlotText(y, '{:.3f}*'.format(pvalue), ha='left'))
|
||||
elif pvalue < 0.05:
|
||||
self.text_right[5].append(EffectPlotText(y, '{:.2f}*'.format(pvalue), ha='left'))
|
||||
else:
|
||||
self.text_right[5].append(EffectPlotText(y, '{:.2f}'.format(pvalue), ha='left'))
|
||||
#if pvalue < 0.05:
|
||||
# self.text_right[6].append(EffectPlotText(y, '*', ha='left'))
|
||||
|
||||
def add_group_heading(self, y, label):
|
||||
self.text_left[0].append(EffectPlotText(y, label, ha='right', fontweight='medium'))
|
||||
|
||||
def _width_of(self, text):
|
||||
txt = self.ax.text(9999, 9999, text, in_layout=False, transform=self.ax.transAxes)
|
||||
txt_width_px = txt.get_window_extent(renderer=self.fig.canvas.get_renderer()).width
|
||||
txt_width_in = self.fig.dpi_scale_trans.inverted().transform([txt_width_px, 0])[0]
|
||||
txt.remove()
|
||||
return txt_width_in
|
||||
|
||||
def render(
|
||||
self,
|
||||
width=4,
|
||||
xscale='log', xlim=(0.5, 4), xticks=['0.5', '1', '2', '4'], minorticks=[],
|
||||
):
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
fig_height = 0.3 * max(d.y for d in self.data) + 0.2
|
||||
|
||||
self.fig, self.ax = plt.subplots(figsize=(width, fig_height))
|
||||
if xscale == 'log':
|
||||
self.ax.axvline(1, color='grey', linewidth=1)
|
||||
else:
|
||||
self.ax.axvline(0, color='grey', linewidth=1)
|
||||
|
||||
self.ax.set_xscale(xscale)
|
||||
self.ax.set_xlim(*xlim)
|
||||
self.ax.set_xticks([float(x) for x in xticks])
|
||||
self.ax.set_xticks(minorticks, minor=True)
|
||||
self.ax.set_xticklabels(xticks)
|
||||
self.ax.set_xticklabels([], minor=True)
|
||||
self.ax.set_xlabel(self.xlabel)
|
||||
|
||||
self.ax.set_ylim(-max(d.y for d in self.data) - 1, 0)
|
||||
self.ax.set_yticks([])
|
||||
|
||||
# Render data bars
|
||||
for data in self.data:
|
||||
self.ax.errorbar(x=[data.mean], y=[-data.y], xerr=[[data.mean-data.ci0], [data.ci1-data.mean]], fmt='o', color='C0', capsize=4, capthick=1.5)
|
||||
|
||||
# Left text
|
||||
tmp = self.fig.dpi_scale_trans.inverted().transform(self.ax.transAxes.transform([0, 0]))
|
||||
tmp[0] -= 0.15
|
||||
x = self.ax.transAxes.inverted().transform(self.fig.dpi_scale_trans.transform(tmp))[0]
|
||||
|
||||
for text in self.text_left[0]:
|
||||
y = self.ax.transAxes.inverted().transform(self.ax.transData.transform([1, -text.y]))[1]
|
||||
self.ax.text(x, y, text.text, transform=self.ax.transAxes, va='center_baseline', **text.kwargs)
|
||||
|
||||
# Get width of right columns
|
||||
widths_right = [max(self._width_of(t.text) if not t.skip_width else 0 for t in col) if len(col) > 0 else 0 for col in self.text_right]
|
||||
|
||||
# Right text
|
||||
for i, col in enumerate(self.text_right):
|
||||
for text in col:
|
||||
tmp = self.fig.dpi_scale_trans.inverted().transform(self.ax.transAxes.transform([1, 0]))
|
||||
tmp[0] += sum(self.space_right[0:i+1])
|
||||
tmp[0] += sum(widths_right[0:i]) or 0
|
||||
|
||||
if text.kwargs['ha'] == 'center':
|
||||
tmp[0] += widths_right[i] / 2
|
||||
if text.kwargs['ha'] == 'right':
|
||||
tmp[0] += widths_right[i]
|
||||
|
||||
x = self.ax.transAxes.inverted().transform(self.fig.dpi_scale_trans.transform(tmp))[0]
|
||||
y = self.ax.transAxes.inverted().transform(self.ax.transData.transform([1, -text.y]))[1]
|
||||
|
||||
self.ax.text(x, y, text.text, transform=self.ax.transAxes, va='center_baseline', **text.kwargs)
|
||||
|
|
|
|||
Loading…
Reference in New Issue