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Questions about adding category annotation in pl.paga_path #31

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Yansr3 opened this issue May 2, 2024 · 0 comments
Open

Questions about adding category annotation in pl.paga_path #31

Yansr3 opened this issue May 2, 2024 · 0 comments

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@Yansr3
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Yansr3 commented May 2, 2024

Hello,

I'm trying to use plot heat map along trajectory with pl.paga_path function. Besides groups_key and pseudotime, I want to add another annotation "sample" in the heat map. However, with only four unique category value in the "sample" column, I got more than four colours in the heatmap annotation. I am wondering if there is any suggestions on adding category annotation in pl.paga_path heatmap.

sc.pl.paga_path(
        adata,
        path,
        ['GATA1','GATA2'],
        show_node_names=False,
        ytick_fontsize=12,
        left_margin=0.15,
        n_avg=50,
        annotations=["dpt_pseudotime","sample"],
        show_yticks=True,
        show_colorbar=False,
        color_map="inferno",
        groups_key="cell_type",
        color_maps_annotations={"dpt_pseudotime": "viridis", "sample": "tab20"},
        normalize_to_zero_one = True
    )
image
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