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PIASO

Colour palettes

Built-in color palettes in PIASO

PIASO provides a diverse selection of discrete color palettes and continous color plattes.

To use the built-in colors in PIASO, you can set the palette=piaso.pl.color.d_color1 for the discrete colors, and cmap=piaso.pl.color.c_color1 for the continuous colors in sc.pl.umap, piaso.pl.plot_embeddings_split or other functions. This notebook aims to display the available choices in both discrete and continuous color maps.

import piaso
import piaso
import scanpy as sc
import numpy as np
import matplotlib.pyplot as plt
import warnings
import piaso.plotting.color as color
sc.set_figure_params(dpi=80,dpi_save=300, color_map='viridis',facecolor='white')
from matplotlib import rcParams
rcParams['figure.figsize'] = 4, 4
warnings.simplefilter(action='ignore', category=FutureWarning)

Load the data

The 20k subsampled snRNA-seq data from Allen SEA-AD project is available in google drive: https://drive.google.com/file/d/1nH-CRaTQFxJ5pAVpy8_hUQn1nrIcakq2/view?usp=drive_link.

The original data is available in https://portal.brain-map.org/explore/seattle-alzheimers-disease.

adata = piaso.data.load_dataset("sea_ad_mtg_20k")
adata

Discrete color palettes

palettes = [c for c in vars(color) if c.startswith('d_')]
n = len(palettes)
ncol = 4
nrow = None
row_size, col_size = 2.4, 2.4
if ncol is None:
        nrow = int(np.sqrt(n))
        ncol = int(np.ceil(n / nrow))
else:
    nrow = int(np.ceil(n / ncol))


fig, axs = plt.subplots(nrow, ncol, dpi=96, figsize=(ncol * col_size, nrow * row_size))


c = 0
for i in range(len(axs)):
    for j in range(len(axs[0])):
        if c < n:
            palette_value = getattr(color, palettes[c], None)


            sc.pl.embedding(adata,
                            basis='X_umap',
                            color=['Subclass'],
                            palette=palette_value,
                            cmap='Spectral_r',
                            size=3,
                            frameon=False,
                            ax=axs[i][j],
                            title='piaso.plotting.color.'+str(palettes[c]+f' - {len(getattr(color, palettes[c], None))} colors'),
                            legend_loc=None,
                            show=False)
            axs[i][j].title.set_size(9)
        else:
            axs[i][j].set_visible(False)
        c += 1
plt.suptitle("Selection of discrete color palettes")
plt.tight_layout()
plt.show()
output

Continuous color palettes

palettes = [c for c in vars(color) if c.startswith('c_')]
n = len(palettes)
ncol = None
nrow = None
row_size, col_size = 2.3, 2.3
if ncol is None:
        nrow = int(np.sqrt(n))
        ncol = int(np.ceil(n / nrow))
else:
    nrow = int(np.ceil(n / ncol))


fig, axs = plt.subplots(nrow, ncol, dpi=96, figsize=(ncol * col_size, nrow * row_size))


c = 0
for i in range(len(axs)):
    for j in range(len(axs[0])):
        if c < n:
            palette_value = getattr(color, palettes[c], None)


            sc.pl.umap(adata,
                       color=['GAD1'],
                       cmap=palette_value,
                       size=15,
                       frameon=False,
                       ax=axs[i][j],
                       title='piaso.plotting.color.'+str(palettes[c]),
                       legend_loc=None,
                       show=False)
            axs[i][j].title.set_size(9)
        else:
            axs[i][j].set_visible(False)
        c += 1
plt.suptitle("Selection of continuous color palettes")
plt.tight_layout()
plt.show()
output