CHANGELOG.md

In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

• 2023-11-21 v0.1.0

  • BREAKING CHANGES
    • Completely re-writes plot_read_depth().
      • allows users to plot read depth with a variable on the X axis and a colour parameter
      • users can access the old function with plt_read_depth() temporarily, but this will be removed before the next full release.
    • rank_abund() is broken and is no longer exported. Please file a bug report if you were using this function.
  • exports order_taxa(), by request
  • makes prop_tax_down() slightly more efficient by checking up front if there is nothing to do.
  • deprecates order_levs() because it isn't used anywhere. Its intended function is performed by order_taxa().
  • introduces visual and automatic testing of the new plot_read_depth() function.
  • in plot_tax_bar()
    • the legloc argument is now passed directly to ggplot2::theme(legend.position) and can take any value that can take.
    • added a r_ticks argument. FALSE by default (default behaviour is unchanged). If TRUE, the tick text on the x-axis is rotated 90 degrees and reads down to up.
    • introduced improved functionality when a custom colour vector is used, with and without names
    • introduce a leglen option to allow the user to limit how many taxa are displayed in the legend without removing any taxa from the plot.
    • soft-deprecate the yscale argument. Will stop supporting non-linear y-axes soon
    • improve error when the rank argument is missing from the input dat frame
    • introduce a warning when the per-sample abundaces sum to greater than 1 but the mean argument is not set to TRUE.
    • prep the function so I can stop exporting the whole ggplot2 namespace
  • introduce lifecycle management with the lifecycle() package
  • start using roxygen2md to use Markdown in documentation.
  • introduce the benchmark folder which contains "good" plotting outputs against which new versions of the package can be tested. Created a .Rmd file in that folder which tests plot_tax_bar().
  • remove the files that held the old colour vectors

• 2023-04-14 v0.0.1 (was v1.0.1)

  • The multiple colour vectors have been replaced with a single object, tax_colours, which will cycle if there are more than 30 taxa. Having more than 30 distinguishable colours is not possible anyway.
  • A bunch of under-the hood reorganization: Functions have been moved to their own .R files or grouped into files with their internal helpers
  • A test suite using testthat has been introduced to catch future problems
  • rename default git branch to main
  • rationalize the versioning system based on guidelines from the r-pkgs book

• 2022-01-11 v0.0.0 (was v1.0)

  • Major bug fix
  • this package has seen minimal changes since January of 2018 when it was first written; however, in April of 2020 there was a major change in the functionality of the right_join() function in the dplyr package contained within the tidyverse suite of packages. This change broke the sorting of taxa relative to OTUs/ASVs when running the function dbig_genera() which is called by default when you run prop_tax_down().
  • Whether you were affected by this bug will depend on if you have updated dplyr to version 1.0.0. or later. You can check your current version of dplyr by running packageVersion('dplyr') in your R console.
  • If you ran prop_tax_down() on your data after April of 2020, and you did not have the dbig = FALSE flag set, your taxon assignments were effectively randomized. Any analyses that relied on taxon assignment (e.g. differential abundance analyses like DESeq, ANCOM, aldex, etc. or visualizations like taxa bar charts) will be incorrect and need to be re-run.
  • Estimates of alpha and beta diversity, PCoA plots, PERMANOVA tests, and placement of samples on UPGMA trees are taxon-insensitive, and are not affected by this bug.
  • Regardless of which version of dplyr you are currently running, it is highly recommended that you update to this version of the aftersl1p package ASAP. The current fix will work with versions of dplyr from before and after the change.

JCSzamosi/aftersl1p documentation built on July 3, 2025, 8:37 p.m.