diff --git a/libhts/libhts.py b/libhts/libhts.py index 45b9f6e5e8317b0cc6322d336d22b3fa573feff6..b7fcf2f4f647b09ed85d60a775c7245a5bdea5bf 100644 --- a/libhts/libhts.py +++ b/libhts/libhts.py @@ -15,7 +15,20 @@ import pandas as pd from scipy.stats.stats import pearsonr, linregress # To compute geometric mean from scipy.stats.mstats import gmean +import matplotlib as mpl import matplotlib.pyplot as plt +# https://stackoverflow.com/a/42768093/1878788 +from matplotlib.backends.backend_pgf import FigureCanvasPgf +mpl.backend_bases.register_backend('pdf', FigureCanvasPgf) +TEX_PARAMS = { + "text.usetex": True, # use LaTeX to write all text + "pgf.rcfonts": False, # Ignore Matplotlibrc + "pgf.texsystem": "lualatex", # hoping to avoid memory issues + "pgf.preamble": [ + r'\usepackage{color}' # xcolor for colours + ] +} +mpl.rcParams.update(TEX_PARAMS) import seaborn as sns from rpy2.robjects import r, pandas2ri, Formula, StrVector as_df = r("as.data.frame") @@ -476,6 +489,7 @@ def plot_scatter(data, y_range=None, axes_style=None): fig, ax = plt.subplots() + # ax.set_adjustable('box') # First plot the data in grey data.plot.scatter( x=x_column, y=y_column,