fantaxtic-deprecated: Deprecated functions in package 'fantaxtic'.

In gmteunisse/Fantaxtic: Fantaxtic - nested bar plots for phyloseq data

Deprecated functions in package fantaxtic.

Description

The functions listed below are deprecated and will be defunct in the near future. When possible, alternative functions with similar functionality are also mentioned. Help pages for deprecated functions are available at help("<function>-deprecated").

Usage

get_top_taxa(
  physeq_obj,
  n,
  relative = TRUE,
  discard_other = FALSE,
  other_label = "Other"
)

gen_palette(clr_tbl, clr_pal = NULL, base_clr = "#6495ed")

fantaxtic_bar(
  physeq_obj,
  color_by,
  label_by = NULL,
  facet_by = NULL,
  grid_by = NULL,
  facet_type = "wrap",
  bar_width = 0.9,
  facet_cols = 1,
  gen_uniq_lbls = TRUE,
  other_label = NULL,
  order_alg = "hclust",
  color_levels = NULL,
  base_color = "#6495ed",
  other_color = "#f3f3f3",
  palette = NULL
)

gen_colors(n, clr = "#6495ed")

shuffle_colors(clrs)

gen_shades_tints(i, clr = "#6495ed")

gen_uniq_lbls(lbls, sep_char = " ")

name_taxa(
  physeq_obj,
  label = "Unannotated",
  other_label = NULL,
  species = FALSE,
  unique_rank = NULL,
  unique_sep = " "
)

get_top_taxa

For get_top_taxa, use top_taxa or nested_top_taxa.

gen_palette

For gen_palette, use nested_palette in the ggnested package.

fantaxtic_bar

For fantaxtic_bar, use plot_nested_bar.

gen_colors

For gen_colors, use nested_palette in the ggnested package.

shuffle_colors

For shuffle_colors, use nested_palette in the ggnested package.

gen_shades_tints

For gen_shades_tints, use nested_palette in the ggnested package.

gen_uniq_lbls

For gen_uniq_lbls, use name_na_taxa or label_duplicate_taxa.

name_taxa

For name_taxa, use name_na_taxa or label_duplicate_taxa.

gmteunisse/Fantaxtic documentation built on June 7, 2024, 8:47 a.m.