\n",
"
Current ordering exceptions
\n",
"
Some functions still retain input order or sort by counts. In particular,\n",
"n_proteins_per_sample can retain row order within groups, and\n",
"n_samples_per_category sorts by counts by default. Their current\n",
"order handling can append unlisted items rather than subset\n",
"them. These examples pass complete explicit orders where needed; consult\n",
"each function's API before relying on subsetting.
\n",
"
\n",
"
Missing values are not measured zeros
\n",
"
Intensity plots generally omit missing measurements; completeness and\n",
"detection plots count their absence. Measured zeros usually remain valid\n",
"observations unless a function's zero-handling option says otherwise.\n",
"The binary heatmap uses a detection threshold and needs an explicit\n",
"missing-value encoding; the correlation heatmap requires complete input\n",
"or a fill value. We explain those choices alongside their examples.\n",
"Missing sample annotations are a separate issue: functions may reject,\n",
"omit, or display them as a missing category. UpSet requires nonmissing\n",
"category labels.
\n",
"