CODEWITHSUNDEEP
pythongridvisualizationscanpytsne
minoo
minoo

Reputation: 575

grid arrange tsne plots from a for loop in scanpy using matplotlib

I want to pu together generated tsnes from the loop below:

import scanpy as sc
import seaborn as sns
import matplotlib.pyplot as plt

# Subset the data by condition
conditions = adata_all.obs['condition'].unique()

# Create a grid of subplots with 1 row and 3 columns
fig, axes = plt.subplots(1, 3, figsize=(12, 4), sharex=True, sharey=True)

for i, condition in enumerate(conditions):
    adata_sub = adata_all[adata_all.obs['condition'] == condition]

    # Run t-SNE
    sc.tl.tsne(adata_sub)

    # Plot t-SNE with LNP color and condition facet in the appropriate subplot
    sc.pl.tsne(adata_sub, color='CD11b', palette=cmap, title=condition, ncols=1, ax=axes[i])
    
# Save the figure
plt.savefig('tsne_plots.png', dpi=300)

I have three condition, like this

conditions: ['AB', 'AC', 'AD']
Categories (3, object): ['AB', 'AC', 'AD'].

But in the output only the first tsne is drawn and the last two are empty plots. What is the problem?

Upvotes: 0

Views: 342

Answers (1)

minoo
minoo

Reputation: 575

This is the correct answer:

import scanpy as sc
import matplotlib.pyplot as plt

# Get unique conditions
conditions = adata_all.obs['condition'].unique()

# Create figure with subplots for each condition
fig, axes = plt.subplots(1, len(conditions), figsize=(12, 4), sharex=True, sharey=True)

# Loop over conditions and plot t-SNE with CD11b color for each
for i, condition in enumerate(conditions):
    # Subset data for current condition
    adata_sub = adata_all[adata_all.obs['condition'] == condition]
    
    # Compute t-SNE
    sc.tl.tsne(adata_sub)
    
    # Plot t-SNE with CD11b color
    sc.pl.tsne(adata_sub, color='CD11b', size=10, color_map='turbo', title=condition, show=False, ax=axes[i])
    
# Save and show the figure
fig.tight_layout()
fig.savefig('tsne_plots.png', dpi=300)
plt.show()

Upvotes: 0

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