scipy-yli/yli/graphs.py

#   scipy-yli: Helpful SciPy utilities and recipes
#   Copyright © 2022–2024  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
	
	plt.rcParams['font.family'] = 'Helvetica Neue LT Std'
	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'))
		
		self.fig = None
		self.ax = None
	
	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
		
		if self.fig is None or self.ax is None:
			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)