The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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.