rabuplot: Relative Abundance Plot
In jstokholm/rabuplot: Relative Abundance Plot

View source: R/rabuplot.R

rabuplot

R Documentation

Relative Abundance Plot

Description

For creating nice microbiome plots

Usage

rabuplot(
  phylo_ob,
  predictor = "none",
  type = "genus",
  relative_abun = TRUE,
  id = NULL,
  xlabs = "Relative abundance (%)",
  ylabs = "Average relative abundance",
  main = "Relative abundance plot",
  violin = TRUE,
  violin_scale = "width",
  legend_title = predictor,
  N_taxa = NULL,
  By_median = TRUE,
  no_other_type = FALSE,
  legend_names = NULL,
  Time = "Time",
  Timepoint = NULL,
  Strata = NULL,
  Strata_val = "1",
  no_legends = FALSE,
  no_names = FALSE,
  italic_names = TRUE,
  Only_sig = FALSE,
  log = TRUE,
  log_max = 100,
  stat_out = FALSE,
  p_val = TRUE,
  p_stars = FALSE,
  stats = "non-parametric",
  p_adjust = FALSE,
  p_adjust_method = "fdr",
  p_adjust_full = FALSE,
  colors = NULL,
  color_by = NULL,
  order = TRUE,
  reverse = FALSE,
  list_taxa = NULL,
  select_taxa = NULL,
  select_type = "genus",
  bar_chart = FALSE,
  bar_chart_stacked = FALSE,
  facet_wrap = NULL,
  facet_label = NULL,
  facet_n = TRUE,
  percent = FALSE,
  order_by = "Time",
  order_val = NULL,
  text_angle_x = 0,
  rank = NULL,
  select_rank = NULL
)

Arguments

`phylo_ob`	Phyloseq object with metadata in sample_data.
`predictor`	Predictor of interest for statistics/plotting in sample_data.
`type`	Taxonomic rank from tax_table, case insensitive; default is "genus".
`relative_abun`	Use relative abundances, else absolute; default is TRUE.
`id`	Define id variable for mixed models.
`xlabs`	X-axis label
`ylabs`	Y-axis label
`main`	Title of plot
`violin`	Use geom_violin for plotting, else boxplot; default is TRUE.
`violin_scale`	Scale option for geom_violin; default is "width".
`legend_title`	Legend title; default is name of predictor.
`N_taxa`	Number of taxa to be plotted; default is 15.
`By_median`	Order plot by median abundances, else mean abundances; default is TRUE.
`no_other_type`	Taxa in lower abundances than top N_taxa, are grouped as "other", this will remove this group from the plot; default is FALSE.
`legend_names`	Define variable names for legend text.
`Time`	Time variable name for longitudinal datasets.
`Timepoint`	Value in variable @Time to select.
`Strata`	Name of variable for stratification;
`Strata_val`	Value in variable @Strata to keep; default is 1.
`no_legends`	Removes legend; default is FALSE.
`no_names`	Removes taxa names; default is FALSE.
`italic_names`	Taxa names will be in italic e.g. usable for family, genus, species levels; default is TRUE
`Only_sig`	Only keep significant taxa; default is FALSE.
`log`	Present plot on a log scale; default is TRUE.
`log_max`	Maximum value of log-axis options:1, 10, 100; default is 100.
`stat_out`	Outputs a data.frame with statistics to Global environment; default is FALSE.
`p_val`	Displays p-values on plot; default is TRUE.
`p_stars`	Shows stars instead of p-values; default is FALSE.
`stats`	Select type of statistical test; options: "non-parametric", "parametric", "mixed", "mgs_feature", "maaslin2"; default is "non-parametric".
`p_adjust`	adjust p-values; default is "FALSE.
`p_adjust_method`	options: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"; default is "fdr".
`p_adjust_full`	correction applied for all taxa in the dataset; default is FALSE.
`colors`	define list of colors for plot. If not color brewer will be used; default is NULL.
`color_by`	define taxonomic rank to color by; default is NULL.
`order`	Order by abundance, else alphabetically; default is TRUE.
`reverse`	Flip taxa order; default is FALSE.
`list_taxa`	A list of specific taxa names to be analyzed; default is NULL.
`select_taxa`	Choose all taxa from one or more taxonomic variables, eg. "Staphylococcus" or "Staph" or "coccus" or c("staph",bifido"); default is NULL.
`select_type`	Taxonomic rank of the @select_taxa; default is "genus".
`bar_chart`	Choose to make bar chart; default is FALSE.
`bar_chart_stacked`	Produce stacked bar chart; default is FALSE
`facet_wrap`	Facet wrap chart by variable; eg. Time; default is NULL.
`facet_label`	Facet wrap labels; default is NULL.
`facet_n`	Show n for each facet; default is TRUE.
`percent`	Print percentages on bar chart; default is FALSE.
`order_by`	Choose variable to order the selected taxa by; eg. Time; default is Time.
`order_val`	Choose value for @order_by; default is NULL.
`text_angle_x`	Choose value for rotation of axis-text; default is 0.
`rank`	Taxonomic rank from tax_table, replaces "type", case insensitive; default is "genus".
`select_rank`	Taxonomic rank of the @select_taxa, replaces "select_type"; default is "genus".