Umap shapes different for the same dataset

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1

Hi,

I generated two umaps using the same dataset but with one I first plotted background cells (in gray) before the cells of interest. The shapes of the two umaps are different.

The code for the regular umap:

sc.pp.highly_variable_genes(
    adata0,
    n_top_genes=2000,
    subset=True,
    layer="counts",
    flavor="seurat_v3",
)
sc.tl.pca(adata0)
sc.pp.neighbors(adata0, n_pcs=30, n_neighbors=20)
sc.tl.umap(adata0, min_dist=0.3)
sc.pl.umap(
    adata0,
    color=["gse"],
    frameon=False,
)

The code for the umap first plotting background cells before the cells of interest:

sc.pp.highly_variable_genes(
    adata0,
    n_top_genes=2000,
    subset=True,
    layer="counts",
    flavor="seurat_v3",
)
sc.tl.pca(adata0)
sc.pp.neighbors(adata0, n_pcs=30, n_neighbors=20)
sc.tl.umap(adata0, min_dist=0.3)
adata = adata0[adata0.obs.clone != 'None']
ax=sc.pl.umap(adata0, show=False, frameon=False, size=5)
adata = adata0[adata0.obs.clone != 'None']
sc.pl.umap(
    adata,
    color=["clone"],
    frameon=False,
    size=5,
    ax = ax,
)

The resulting umap for regular umap:

umap_10x_gse
umap_10x_gse953×409 150 KB

The resulting umap when background cells first plotted:
umap_10x_mixcr_2

As you can see the two umaps have different shapes. Any ideas? Thanks.

2

I just realized the shapes are the same (accounting for bigger dot size).