In [1]:
import scanpy as sc
In [2]:
input_file = "../results/05_prepare_adata_nk_t/adata.h5ad"
In [3]:
# Parameters
input_file = "input_adata.h5ad"
In [4]:
adata = sc.read_h5ad(input_file)
In [5]:
adata_t = adata[adata.obs["cell_type"] != "NK cell", :]

/opt/conda/lib/python3.8/site-packages/anndata/_core/anndata.py:1094: FutureWarning: is_categorical is deprecated and will be removed in a future version.  Use is_categorical_dtype instead
  if not is_categorical(df_full[k]):
In [6]:
sc.pl.umap(adata_t, color="cluster", save="_klrb1.pdf")

WARNING: saving figure to file figures/umap_klrb1.pdf
In [7]:
sc.pl.dotplot(
    adata_t,
    var_names=["CD3D", "CD3E", "CD3G", "CD4", "CD8A", "CD8B", "KLRB1"],
    groupby="cluster",
    swap_axes=True,
    save="klrb1.pdf",
)

WARNING: saving figure to file figures/dotplot_klrb1.pdf
In [ ]: