significance of same dots changes based on plotted clusters in sq.pl.ligrec

[t-a-m-i]

Description

sq.gr.ligrec was used to calculate ligand-receptor statistics for the whole input dataset. However, when plotting the results, the dots for the same interactions differ depending on the clusters selected for plotting. If I only plot clusters 1 and 2 as source and clusters 1, 2, and 3 as target groups, the same dots shown in the graph as being significant (tori) might suddenly become non-significant when I choose to plot clusters 1 and 2 as source and 1 and 2 as target groups.
To my understanding the pvalues shouldn't get modified based on result subsetting. Additionally, when I subset the result["pvalues"] for my own data to the remaining source and target molecules that are being plotted, all should be shown to be significant, but are not in the plot.

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Minimal reproducible example

adata = sq.datasets.seqfish()
sc.pp.normalize_total(adata) 
sc.pp.log1p(adata)

res_test = sq.gr.ligrec(
    adata,
    n_perms=100,
    threshold=0,
    copy=True,
    cluster_key="celltype_mapped_refined",
    use_raw=False
)

sq.pl.ligrec(
    res_test,
    source_groups=["Lateral plate mesoderm","Intermediate mesoderm"],
    target_groups=["Lateral plate mesoderm","Intermediate mesoderm",'Allantois'],
    means_range=(0.5, np.inf),
    alpha=0.005,
    swap_axes=True,
)

# vs. 

sq.pl.ligrec(
    res_test,
    source_groups=["Lateral plate mesoderm","Intermediate mesoderm"],
    target_groups=["Lateral plate mesoderm","Intermediate mesoderm"],
    means_range=(0.5, np.inf),
    alpha=0.005,
    swap_axes=True,
)

# in the second plot for example the pair "WNT5A" and "FZD2" should all be significant like seen here, but is not in the plot
# Target clusters to keep
targets = ["Lateral plate mesoderm","Intermediate mesoderm"]

# Filter the columns
filtered_test = res_test["pvalues"].loc[:, 
    res_test["pvalues"].columns.get_level_values('cluster_1').isin(targets) &
    res_test["pvalues"].columns.get_level_values('cluster_2').isin(targets)
]
filtered_test = filtered_test[(filtered_test.index.get_level_values(0) == "WNT5A") & 
                (filtered_test.index.get_level_values(1) == "FZD2")]

filtered_test

Version

python=3.10.16, squidpy=1.6.1

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