Barplot based on ggplot2

plot_barplot(
  object,
  fill = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  alluvial = FALSE,
  top_n = 5,
  show.legend,
  what = c("sum_intensity", "mean_intensity", "median_intensity"),
  na.rm = TRUE,
  relative = TRUE,
  re_calculate_relative = FALSE,
  x = "sample_id",
  color = "balck",
  facet_grid,
  ...
)

# S3 method for microbiome_dataset
plot_barplot(
  object,
  fill = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  alluvial = FALSE,
  top_n = 5,
  show.legend,
  what = c("sum_intensity", "mean_intensity", "median_intensity"),
  na.rm = TRUE,
  relative = TRUE,
  re_calculate_relative = FALSE,
  x = "sample_id",
  color = "balck",
  facet_grid,
  ...
)

Arguments

object: microbiome_dataset
fill: fill for barplot
alluvial: Add alluvial or not.
top_n: default is 5
show.legend: show.legend or not
what: which you want to mutate
na.rm: na.rm
relative: relative intensity or not.
re_calculate_relative: re-calculate relative abundance or not.
x: x axis
color: color for barplot
facet_grid: facet_grid
...: other params

Value

ggplot2 class object

Examples

library(microbiomeplot)
data("global_patterns")
global_patterns %>%
  activate_microbiome_dataset(what = "sample_info") %>%
  filter(SampleType %in% c("Feces", "Mock")) %>%
  plot_barplot(fill = "Phylum")


global_patterns %>%
  activate_microbiome_dataset(what = "sample_info") %>%
  filter(SampleType %in% c("Feces", "Mock")) %>%
  plot_barplot(
    fill = "Phylum",
    relative = TRUE,
    re_calculate_relative = TRUE,
    show.legend = TRUE
  )


global_patterns %>%
  activate_microbiome_dataset(what = "sample_info") %>%
  filter(SampleType %in% c("Feces", "Mock")) %>%
  plot_barplot(fill = "Phylum",
               alluvial = TRUE,
               top_n = 10)


global_patterns %>%
  activate_microbiome_dataset(what = "sample_info") %>%
  filter(SampleType %in% c("Feces", "Mock")) %>%
  plot_barplot(
    fill = "Phylum",
    relative = TRUE,
    re_calculate_relative = TRUE,
    show.legend = TRUE,
    alluvial = TRUE,
    top_n = 10
  )


global_patterns %>%
  activate_microbiome_dataset(what = "sample_info") %>%
  filter(SampleType %in% c("Feces", "Mock")) %>%
  plot_barplot(
    fill = "Phylum",
    relative = TRUE,
    re_calculate_relative = TRUE,
    show.legend = TRUE,
    alluvial = TRUE,
    top_n = 10,
    facet_grid = "SampleType"
  )