phyloseq_long_bargraph: Do a bar graph of top taxo_level or asvs based on the long...

In vaulot/dvutils: A set of utilities

Description

Plot the bar graph and returns a list with a ggplot and a df with the summary of the data

Usage

phyloseq_long_bargraph(
  df,
  n_bars = 30,
  title = "",
  text_scaling = 0.75,
  use_asv = TRUE,
  taxo_level = species,
  taxo_level_fill = division,
  taxo_colors_fill = structure(c("green", "orange", "red", "blue", "brown"), .Names =
    c("Chlorophyta", "Cryptophyta", "Rhodophyta", "Haptophyta", "Ochrophyta"))
)

Arguments

df	Data frame obtained from a phyloseq file using the function phyloseq_transform_to_long
n_bars	numbers of bars to plot
title	Title for the treemap
text_scaling	Scaling for the text of the graph
use_asv	If TRUE use asvs, if FALSE use the taxo_level selected
taxo_level	Taxonomic level to use when use_asv = FALSE (should be between species up to class)
division_colors	Colors to be used for the different divisions

Value

Plot the bargraph Returns a list made of 2 elements

• gg = the bargraph as ggplot

• df = a dataframe with the summarized data

Examples

my_list <- phyloseq_long_asv_bargraph(phyloseq_long, title= "Antartica", n_bars=10, use_asv = FALSE, taxo_level= genus, text_scaling=1)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.