diff --git a/CHANGELOG.md b/CHANGELOG.md index 4fbdf6a..20c5815 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,12 +1,12 @@ -* 2023-08-03 v0.0.1.9002 (development update) +* 2023-11-21 v0.1.0 * **BREAKING CHANGES** - * Completely re-writes `plot_read_depth()`. + * **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. + * **`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. @@ -14,8 +14,6 @@ function is performed by `order_taxa()`. * introduces visual and automatic testing of the new `plot_read_depth()` function. - -* 2023-04-25 v0.0.1.9001 (development update) * in `plot_tax_bar()` * the `legloc` argument is now passed directly to `ggplot2::theme(legend.position)` and can take any value that can take. diff --git a/DESCRIPTION b/DESCRIPTION index 73a1790..7f6285c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: AfterSl1p Type: Package Title: Generate Summary Graphics and Basic Analysis of 16s Data -Version: 0.0.1.9001 +Version: 0.1.0 Author: J. C. Szamosi and Shahrokh Shekarriz Authors@R: c(person("JC", "Szamosi", email = "szamosjc@mcmaster.ca", role = c('aut','cre')), diff --git a/R/plot_read_depth.R b/R/plot_read_depth.R index acf9ac9..73938ab 100644 --- a/R/plot_read_depth.R +++ b/R/plot_read_depth.R @@ -178,7 +178,7 @@ prd_clrs = function(sample_sum_df, cvar, clrs){ #' @param physeq A phyloseq object #' @export plt_read_depth = function(physeq){ - lifecycle::deprecate_soft('0.0.1.9002', 'plt_read_depth()', + lifecycle::deprecate_soft('0.1.0.', 'plt_read_depth()', 'plot_read_depth()', details = paste("This is the old version of", "plot_read_depth(), and will be", diff --git a/R/plot_tax_bar.R b/R/plot_tax_bar.R index eff48da..3a102ca 100644 --- a/R/plot_tax_bar.R +++ b/R/plot_tax_bar.R @@ -45,7 +45,7 @@ plot_tax_bar = function(taxa_df,rank,colours = NULL, means = FALSE, r_ticks = FALSE, leglen = NULL){ # Lifecycle Management if (yscale != 'lin'){ - lifecycle::deprecate_warn('0.0.1', 'plot_tax_bar(yscale)', + lifecycle::deprecate_warn('0.1.0', 'plot_tax_bar(yscale)', details = paste('The ability to set non-linear y-axis', 'scaling will be removed soon.')) } diff --git a/R/utils.R b/R/utils.R index 7b74dba..6bfc419 100644 --- a/R/utils.R +++ b/R/utils.R @@ -21,7 +21,7 @@ #' @param f2 The factor to use when re-ordering `f1`. #' @export order_levs = function(f1,...){ - lifecycle::deprecate_warn('0.0.2', 'order_levs()') + lifecycle::deprecate_warn('0.1.0', 'order_levs()') # if (is.numeric(f2)){ # ord = order(...)