Heatmaps / Presence/absence heatmap
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Each row is an item (gene, taxon, variant…) and each column a sample or set; dark cells are present, light cells absent and grey cells missing.
Numbers are turned into presence when they exceed the threshold, so with a threshold of 0 any positive count is present; text cells may use yes/no, present/absent or +/−.
“Jaccard clustering” places columns that share many items, and rows with similar patterns, next to each other; “by frequency” puts the most common rows and columns at the top left, which suits core-versus-unique questions.
The bars on the right show in how many columns each row is present, making shared (high count) and unique (count 1) items easy to spot.
Ordering: average-linkage hierarchical clustering on Jaccard distances (1 − intersection / union).
Up to 2,000 rows are drawn.
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