VISTA follows the Bioconductor deprecation contract: a renamed argument warns for one release, becomes defunct in the next, and is removed in the one after. Deprecated arguments keep working exactly as before while they warn.
Details
The table below is generated from the package's internal registry, so it is
always in sync with the code. Warnings are classed
c("vista_deprecated_arg", "deprecatedWarning") and are throttled so they
will not flood a loop: by default each is shown at most once every eight
hours per argument. Set options(vista.deprecation_frequency = "once") for
once per session, or "always" to see every occurrence.
To silence them while you migrate:
suppressWarnings(get_corr_heatmap(v, show_corr_values = TRUE))To find every deprecated call in your own scripts, promote the warnings to errors:
options(warn = 2)Inspecting the registry
The authoritative list lives in the package itself rather than being duplicated here, so it cannot drift out of date. Print it with the example below, or filter it to the function you are migrating.
Defaults that will change
A default that is going to change is announced one release ahead, so
results do not move without warning. The old default stays in force until
the release named in changes_in; until then, a call that relies on it (by
not setting the argument, or passing NULL) prints a message classed
vista_default_change, throttled like the warnings above.
Setting the argument explicitly, to either value, keeps results stable
across the change and silences the message. In VISTA 1.2.0 this applies to
edger_test, which moves from "LRT" (likelihood-ratio test) to "QL"
(quasi-likelihood F-test) in VISTA 1.4.0, in create_vista(),
run_edger_analysis(), benchmark_vista_equivalence() and
validate_vista_deep().
Examples
# The full table of deprecated arguments and their timelines
VISTA:::.vista_deprecations()[, c("fun", "old_arg", "new_arg", "defunct_in")]
#> fun old_arg new_arg defunct_in
#> 1 get_corr_heatmap show_corr_values label 1.4.0
#> 2 get_corr_heatmap col_corr_values label_color 1.4.0
#> 3 get_volcano_plot col_up colors 1.4.0
#> 4 get_volcano_plot col_down colors 1.4.0
#> 5 get_volcano_plot col_other colors 1.4.0
#> 6 get_volcano_plot col_others colors 1.4.0
#> 7 get_volcano_plot lab_size label_size 1.4.0
#> 8 get_pca_plot sample.seed 1.4.0
#> 9 get_pca_plot use_vista_colors use_group_colors 1.4.0
#> 10 get_mds_plot use_vista_colors use_group_colors 1.4.0
#> 11 get_umap_plot use_vista_colors use_group_colors 1.4.0
#> 12 get_expression_barplot facet_scale facet_scales 1.4.0
#> 13 get_expression_lollipop facet_scale facet_scales 1.4.0
#> 14 get_corr_heatmap cluster_by order_by 1.4.0
#> 15 get_celltype_group_dotplot error errorbar 1.4.0
#> 16 get_deg_count_pieplot label label_type 1.4.0
#> 17 get_deg_count_donutplot label label_type 1.4.0
#> 18 get_expression_boxplot comparisons stat_comparisons 1.4.0
#> 19 get_expression_lineplot comparisons stat_comparisons 1.4.0
#> 20 get_expression_violinplot comparisons stat_comparisons 1.4.0
#> 21 get_expression_barplot comparisons stat_comparisons 1.4.0
#> 22 get_pca_plot top_n_genes top_n 1.4.0
#> 23 get_mds_plot top_n_genes top_n 1.4.0
#> 24 get_umap_plot top_n_genes top_n 1.4.0
#> 25 get_expression_lollipop line_size linewidth 1.4.0
#> 26 get_foldchange_lollipop line_size linewidth 1.4.0
#> 27 get_expression_violinplot value_transform log_transform 1.4.0
#> 28 get_expression_lineplot value_transform log_transform 1.4.0
# Or just the one function you are migrating
reg <- VISTA:::.vista_deprecations()
reg[reg$fun == "get_corr_heatmap", c("old_arg", "new_arg", "defunct_in")]
#> old_arg new_arg defunct_in
#> 1 show_corr_values label 1.4.0
#> 2 col_corr_values label_color 1.4.0
#> 14 cluster_by order_by 1.4.0
# Defaults that will change, and when
VISTA:::.vista_default_changes()[, c("fun", "arg", "old_default", "new_default", "changes_in")]
#> fun arg old_default new_default changes_in
#> 1 create_vista edger_test LRT QL 1.4.0
#> 2 run_edger_analysis edger_test LRT QL 1.4.0
#> 3 benchmark_vista_equivalence edger_test LRT QL 1.4.0
#> 4 validate_vista_deep edger_test LRT QL 1.4.0