Covariate layer #19
Covariate layer #19
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Pull Request Overview
This PR introduces a covariate layer in the header formatting, adds tests and example scripts, updates documentation, and extends utility functions for custom formatting.
- Adds a
format_covariate_headerfunction and integrates it into thetbl_format_header.SE_print_abstractionmethod. - Introduces new unit tests under
tests/testthat/and a standalone debug script. - Updates the README examples and session info, and extends pillar utilities and NAMESPACE imports.
Reviewed Changes
Copilot reviewed 8 out of 9 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/Introduction.R | Deleted outdated introduction vignette |
| tests/testthat/test-header-formatting.R | Added snapshot tests for format_covariate_header |
| test_header_formatting.R | Added standalone debug/example script (should be reviewed) |
| README.md | Updated example output rows and sessionInfo details |
| R/tidyprint_1_utlis.R | Added format_covariate_header and extended formatting logic |
| R/print_methods.R | Adjusted separator row computation and attribute packing |
| R/pillar_utlis.R | Extended pillar___format_comment with strip.spaces |
| NAMESPACE | Added new importFrom entries for dplyr, purrr, etc. |
Comments suppressed due to low confidence (3)
R/pillar_utlis.R:3
- This function now calls
get_extent, butget_extentisn't imported in NAMESPACE; addimportFrom(pillar, get_extent)so the function resolves correctly at runtime.
pillar___format_comment <- function (x, width, strip.spaces = TRUE)
NAMESPACE:19
- Missing imports for newly used functions
pillar::style_subtleandpillar::get_extent; please addimportFrom(pillar, style_subtle, get_extent)to NAMESPACE.
importFrom(cli,col_br_black)
test_header_formatting.R
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| @@ -0,0 +1,139 @@ | |||
| # Test script for header formatting function | |||
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This standalone debug/example script appears to be for local testing; consider removing it or moving it under tests/ so it does not clutter the root directory.
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R/tidyprint_1_utlis.R
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| covariate_indices <- which(printed_colnames %in% covariate_names) | ||
| covariate_widths <- separator_row[printed_colnames[covariate_indices]] |> purrr::map_int(nchar) | ||
| total_covariate_width <- sum(covariate_widths) + length(covariate_widths) + 3 # To compensate the white spaces of the tibble |
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Avoid using unexplained magic numbers like + 3; consider computing the extra spacing based on actual separator characters or document the reason for this offset.
| total_covariate_width <- sum(covariate_widths) + length(covariate_widths) + 3 # To compensate the white spaces of the tibble | |
| # Compute extra spacing dynamically based on separator characters | |
| separator_spacing <- nchar("|") * 2 + 1 # Account for '|' at both ends and one space | |
| total_covariate_width <- sum(covariate_widths) + length(covariate_widths) + separator_spacing |
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R/tidyprint_1_utlis.R
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| header_row[covariate_indices[-1]] <- "" | ||
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| # Add row ID spacing at the beginning | ||
| header_row <- c(paste(rep(" ", number_of_total_rows |> nchar() - 3), collapse = ""), header_row) |
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Calculating row-ID spacing using nchar(number_of_total_rows) - 3 is brittle; consider deriving the padding from the actual row ID width rather than hard-coding - 3.
| header_row <- c(paste(rep(" ", number_of_total_rows |> nchar() - 3), collapse = ""), header_row) | |
| row_id_width <- nchar(total_rows) | |
| header_row <- c(paste(rep(" ", row_id_width), collapse = ""), header_row) |
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| number_of_features, | ||
| number_of_samples, | ||
| assay_names %>% paste(collapse=", ") | ||
| )), after = 1) | ||
| ))) | ||
| # , after = 1) |
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Remove leftover commented-out code snippets to keep the implementation clean and maintainable.
| # , after = 1) |
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…riate_header function; update NAMESPACE accordingly.
stemangiola
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…or format_covariate_header
…int method for SummarizedExperiment to improve design handling and output formatting.
…label alignment and improve overall output presentation.
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