potterae
commented
1 year ago I found that when the seurat object was converted to AnnData, it changed the identities to a number; I made a new column in the metadata of the AnnData object which contained the cell type identities from the associated numbers, and this solved the issue. Thanks.
Hi, thank you for developing this package, it is very useful. I am trying to use this to display info regarding varying cell composition among different conditions / samples. Unfortunately, it displays the cell type as a number and not the actual defined cell type. Is there a way to change this so I can have it display the cell identities, not numbers? This is using an integrated seurat object, converted to AnnData format using SeuratDisk.
The python code is below:
import warnings import importlib warnings.filterwarnings("ignore")
import pandas as pd import pickle as pkl import matplotlib.pyplot as plt import anndata as ad import warnings
from sccoda.util import comp_ana as mod from sccoda.util import cell_composition_data as dat from sccoda.util import data_visualization as viz
adata = ad.read_h5ad("/Immune.h5ad") print(adata)
cov_df = pd.DataFrame({"Stage": ["Severe", "CR", "Improving", "Resolved", "No", "No", "No", "No", "No", "No", "No", "No", "No"]}, index=-removed-) print(cov_df)
data_CR = dat.from_scanpy( adata, cell_type_identifier="Idents", sample_identifier="X", covariate_df=cov_df ) print(data_CR)
Stacked barplot for each sample
viz.stacked_barplot(data_CR, feature_name="samples") plt.show()
Stacked barplot output:
print output, data_CR:
-removed- AnnData object with n_obs × n_vars = 13 × 13 obs: 'Stage' var: 'n_cells'
Thank you!