Implement HorizontalEffectPlot

yli/__init__.py

@@ -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

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)