Covariate layer #19

stemangiola · 2025-06-28T23:36:10Z

No description provided.

Copilot

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_header function and integrates it into the tbl_format_header.SE_print_abstraction method.
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vignettes/Introduction.R	Deleted outdated introduction vignette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, but get_extent isn't imported in NAMESPACE; add importFrom(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_subtle and pillar::get_extent; please add importFrom(pillar, style_subtle, get_extent) to NAMESPACE.

importFrom(cli,col_br_black)

Copilot · 2025-06-28T23:37:41Z

test_header_formatting.R

@@ -0,0 +1,139 @@
+# Test script for header formatting function


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.

Copilot · 2025-06-28T23:37:42Z

R/tidyprint_1_utlis.R


+  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


Avoid using unexplained magic numbers like + 3; consider computing the extra spacing based on actual separator characters or document the reason for this offset.

Suggested change

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

Copilot · 2025-06-28T23:37:42Z

R/tidyprint_1_utlis.R

+  header_row[covariate_indices[-1]] <- ""
+
+  # Add row ID spacing at the beginning
+  header_row <- c(paste(rep(" ", number_of_total_rows |> nchar() - 3), collapse = ""), header_row)


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.

Suggested change

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)

Copilot · 2025-06-28T23:37:42Z

R/tidyprint_1_utlis.R

        number_of_features,
        number_of_samples,
        assay_names %>% paste(collapse=", ")
-      )), after = 1)
+      )))
+      # , after = 1)


Remove leftover commented-out code snippets to keep the implementation clean and maintainable.

Suggested change

# , after = 1)

…bility

…tation

…riate_header function; update NAMESPACE accordingly.

…or format_covariate_header

…int method for SummarizedExperiment to improve design handling and output formatting.

…label alignment and improve overall output presentation.

stemangiola · 2025-08-29T22:36:04Z

@zhanchen this PR I dont think works for arbitrary datasets. I tagged into an issue about the non existance of a variable that counts the table size in its renfered form.

This was not meant to be merged I think. Unless you solved that issue and tested extensively on many datasets.

zhanchen · 2025-08-30T00:45:42Z

@stemangiola
Yes, I fixed the covariate-layer print issue and committed to the branch before the merge.
Now the covariate-layer can align with the covariate column under varying widths and shall be removed when the width is too small and no covariate column was actually printed.

I will test it with datasets in the next couple days.

stemangiola requested a review from Copilot June 28, 2025 23:36

stemangiola linked an issue Jun 28, 2025 that may be closed by this pull request

Explicit covariate compartment #18

Closed

Copilot AI reviewed Jun 28, 2025

View reviewed changes

stemangiola added 6 commits June 29, 2025 09:56

add header

d194680

imperfect placement of the covariate label

9cb0718

more scalable COVRIATE header

cdf094e

Refactor covariate header formatting for improved alignment and scala…

6964037

…bility

Add format_covariate_header function and update NAMESPACE for documen…

59e8d0d

…tation

Remove unused exports and delete obsolete test script for format_cova…

b69627c

…riate_header function; update NAMESPACE accordingly.

stemangiola force-pushed the covariate-layer branch from bb88d85 to b69627c Compare June 28, 2025 23:59

stemangiola and others added 4 commits June 29, 2025 10:00

Update .gitignore, export new functions in NAMESPACE, and add tests f…

a9d0a40

…or format_covariate_header

Enhance NAMESPACE and README with new imports and examples; update pr…

b698bad

…int method for SummarizedExperiment to improve design handling and output formatting.

Refactor header formatting in tbl_format_header to enhance covariate …

e156756

…label alignment and improve overall output presentation.

Bug fixed: covariates indication, factor column error

978e3a6

zhanchen merged commit 978e3a6 into main Aug 29, 2025
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Covariate layer #19

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stemangiola commented Aug 29, 2025

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zhanchen commented Aug 30, 2025 •

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		@@ -0,0 +1,139 @@
		# Test script for header formatting function

-  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

	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)

Covariate layer #19

Covariate layer #19

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Pull Request Overview

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zhanchen commented Aug 30, 2025 •

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