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DESCRIPTION
per CRAN reviewer request.DESCRIPTION.\dontrun{} to \donttest{} in
examples for plot_SBS288() and
plot_guess_pdf() per CRAN reviewer request.man/*.Rd links in README.md
with in-page anchors (#sbs12, #dbs144,
#id166) and added the corresponding gallery sections with
example figures. CRAN’s R-devel pretest of 2.0.36 flagged the original
man/*.Rd links as “Possibly invalid file URIs” because the
rendered Rd files are not present in the installed package._R_CHECK_CRAN_INCOMING_,
_R_CHECK_CRAN_INCOMING_REMOTE_,
_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_, and
_R_CHECK_CRAN_INCOMING_USE_ASPELL_ in
R-CMD-check.yaml so the GitHub matrix runs the same
incoming-feasibility checks CRAN’s pretest does.Title to title case,
reworded Description to not start with the package name,
added trailing slash to the pkgdown site URL, and restored the
ubuntu-latest / oldrel-1 row to the R-CMD-check GitHub
Actions matrix.plot_ID476, plot_ID476_right,
and plot_SBS1536 examples in \donttest{} so
the shared bar_plots and heatmap_plots Rd
pages run in under the CRAN 5-second-per-Rd example-runtime limit. The
examples are unchanged and remain user-runnable via
example(plot_ID476, run.donttest = TRUE).id89_figlabels() from R/plot_ID89.R
to its own file (R/id89_figlabels.R) and exported it.Del(2,):R(5,) is now rendered as
L(2, )R(5+) instead of L(2, ):R(5+)).
Re-blessed regression hashes and visual reference PNGs for
plot_ID89 / plot_ID89_peaks, and regenerated
the README example_ID89.png.stop_at_9 argument from
plot_ID89(), plot_ID476(), and
plot_ID476_right(). The package now always uses the “open”
(N+) repeat-tract label style; users who needed the old
(N-9) capped style should recognise that their upstream
indel classifications may have been trimmed at 9. In
plot_ID89() the flag is kept as an internal constant
(stop_at_9 <- FALSE); in the two ID476 variants it was
unused and has been dropped cleanly.plot_ID89(): the internal
IndelType column now derives from
catalog_row_order()$ID89 instead of an inline 89-element
literal, giving a single source of truth for channel names.id89_figlabels() derives x-axis
tick labels algorithmically from the canonical IndelType
strings. Open-ended repeat tracts are rendered as (N+)
(e.g. T(8+), C(7+), R(5+)) rather
than the former (8,9) / (7,9) notation;
sub-block bracket labels also use the (N+) style.Indel3 column from
plot_ID89() and from type_476_indel_type()
(never read).stop_at_9 default in plot_ID89()
from TRUE to FALSE; the plot data is
unchanged, but (8+) now communicates that the user must
know their upstream trimming.plot_ID89 with peak labels) and a corresponding
plot_ID89_peaks entry in tests/visual/.plot_ID89 and plot_ID89_peaks to match the new
label style.plot_title_cex default at 1.0 and
axis_*_cex defaults (axis_text_x_cex = 0.5,
axis_title_x_cex = 0.8, axis_text_y_cex = 0.7,
axis_title_y_cex = 0.8) across all bar-plot functions.title_outside_plot = FALSE argument on every
bar-plot function. By default the plot title is now drawn inside the
panel (in the plot_ID83 style) via a shared
add_plot_title() helper. Set TRUE for the
ggtitle()-above-the-panel layout previously used by
plot_ID89, plot_ID476, and
plot_ID476_right.plot_SBS288,
title_outside_plot = FALSE prepends plot_title
to each strand label (“Template”, “Non-template”, “Not-transcribed”);
TRUE keeps the previous
patchwork::plot_annotation() overall title.plot_ID89, plot_ID476, and
plot_ID476_right now position the inside title in the gap
between the tallest bar and the colored block strip.grid = FALSE argument on every bar-plot function
(added to plot_SBS12, plot_DBS144,
plot_ID89, plot_ID476,
plot_ID476_right). Default is now FALSE
everywhere (previously TRUE in plot_SBS96,
plot_SBS192, plot_DBS78,
plot_ID83, plot_ID166).development/regenerate_readme_figures.R for
rebuilding the man/figures/example_*.png set after visual
changes.show_extra_top_bar parameter from
plot_ID89() and plot_ID89_pdf()plot_ID89()plot_89() retains show_extra_top_bar for
backward compatibility but ignores itplot_ID83_pdf() and plot_ID89_pdf()
calling the new-style plot functionsplot_83_pdf() and
plot_89_pdf()plot_89: automatically adjust setyaxis
upward when it is less than 1.1 times the highest bar, preventing bars
from being clipped by the y-axis limit.@examples to all exported functions for
CRAN compliance..claude-trace and tests/visual to
.Rbuildignore.R CMD check passes with 0 errors, 0 warnings, 0
notes.plot_SBS96, plot_SBS192,
plot_SBS12, plot_SBS288,
plot_DBS78, plot_DBS144, plot_83,
plot_89, plot_476,
plot_ID166.plot_guess() and
plot_guess_pdf().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.