CODEWITHSUNDEEP
pythonscanpy
pythonbeginner
pythonbeginner

Reputation: 63

How to plot proportion of cells in each cluster with scanpy?

I am analyzing single cell data with scanpy. I have using leiden to cluster my samples. I would like to figure out how many cells are in each cluster and plot the proportion of cells for each cluster.

I have found the code shown below from this link https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_04_clustering.html

tmp = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['type'], normalize='index')
tmp.plot.bar(stacked=True).legend(loc='upper right')

However, I am not sure how to adjust it for my data because I don't have 2 groups. I just want a graph that shows that cluster 1 is 10% of the total cells, cluster 2 is 20% etc.

Thank you

Upvotes: 0

Views: 1076

Answers (1)

nobot
nobot

Reputation: 93

If you just want to show proportion of clusters among all cells maybe you can use a pie chart?

val_counts = adata.obs['leiden'].value_counts()
pd.DataFrame(val_counts).plot.pie(y = 'count')
plt.legend(loc='center left', bbox_to_anchor=(1, 0.5));

Upvotes: 0

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