Split dotplot

[brianpenghe]

I was wondering whether it is possible to plot this split dotplot (in this case, half of a dot represents mRNA levels while the other half about protein)?

This is useful in two places: 1. when we are visualizing mRNA and protein levels of a same group of genes 2. when we are comparing two conditions (control PBMC vs stimulated PBMC etc.). Because it would avoid duplicating the gene/cell type names and save half the space compared to this one:

Thanks

[LeticiaRojas]

Hi guys!
Any alternative to go around this? I'm also looking for an option in scanpy dotplot to split by condition.
Thanks

[GirayEryilmaz]

Until this gets implemented I have this:

import pandas as pd
import scanpy as sc
from matplotlib import pyplot as plt

# get data
adata = sc.datasets.pbmc68k_reduced()

# prepare df
metadata1 = 'phase'
metadata2 = 'bulk_labels'
gene = 'CD8A'

def mean_and_fract_cells_by_gene(df, gene):
    fraction_of_cells = (df[gene]>0).sum()/len(df)
    mean = df.mean(numeric_only=True)[0]
    return pd.Series({'fraction_of_cells' : fraction_of_cells*100, 'Mean': mean})

df = sc.get.obs_df(adata, keys=[gene, metadata1, metadata2])

df = df.groupby([metadata1,metadata2]).apply(lambda df: mean_and_fract_cells_by_gene(df, gene=gene)).reset_index()

# plot
fig, ax = plt.subplots(figsize = (5, 5))
df.plot.scatter(x=metadata1, y=metadata2, s='fraction_of_cells', c='Mean', cmap='Reds', edgecolors='grey', ax=ax);
ax.tick_params(axis='x', rotation=90)
ax.set_title('Dotplot')
fig.set_tight_layout(True)
fig.savefig('dotplot.png', facecolor='white')

Which outputs:

If anyone can add the "Fraction of cells in group" legend too, that would be appreciated.