feat: port create_lr_dataframe() into the package - #97
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Long-format reshape of the three matrices produced by calculate_lr_scores() / calculate_gene_set_score() / calculate_gene_set_specificity() — pivots them into a tidy data frame keyed by (interaction, source_cell_type, target_cell_type) with merged ligand/receptor gene names from the lrpairs reference. The function previously lived in the SpaceMarkers_Protocol repo's R/protocol-helpers.R; Orian asked that we promote it to the package proper since (a) it's the natural tidy view of the package's own LR-scoring outputs, (b) all the dependencies (reshape2, dplyr) are already in Imports, and (c) it's per-sample, not multi-sample orchestration. Two cleanups vs. the protocol-helpers version: - Drop the unconditional `lrscores[is.na(lrscores)] <- 0` line. That was the silent-zero footgun that masked the all-NaN LR matrix bug we hit during the protocol render. NAs now propagate to the score column; callers can filter or impute explicitly. - Doc/code mismatch on @return columns: original docstring listed 8 columns; function returned 9 (source_to_target was tacked on at the end). Updated docstring to list all 9. Also added a @note flagging the parsing constraint: cell-type names must not contain "_to_" or "_and_" (the function uses those as delimiters when reconstructing source/target from the joined-key string). Tests cover the round-trip on a small fixture plus an explicit NA-preservation check (the regression we just fixed).
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Summary
Promotes `create_lr_dataframe()` from the protocol-helpers vendor file into the package proper, per Orian's request. It's the natural tidy view of `calculate_lr_scores` / `calculate_gene_set_score` / `calculate_gene_set_specificity` output — those are already in the package, so the consumer should be too.
Two cleanups vs. the original
Constraint flagged via `@note`
The function reconstructs `source_cell_type` / `target_cell_type` from a joined string key (`andto`), so cell-type names must not contain `to` or `and` substrings. Documented at the top of the manpage.
Tests
`devtools::test(filter = "create_lr_dataframe")` → 6 PASS, 0 FAIL.
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