phyloseq_nmds: 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_nmds(
  ps,
  title = "",
  env_parameters = c("temperature", "salinity", "Chla", "NO3", "PO4", "Si"),
  classifying_parameters = c("fraction_name", "season"),
  sample_color = fraction_name,
  sample_shape = season,
  sample_label = sample_label,
  taxo_level = division,
  taxo_colors = structure(c("green", "orange", "red", "blue", "brown"), .Names =
    c("Chlorophyta", "Cryptophyta", "Rhodophyta", "Haptophyta", "Ochrophyta"))
)

Arguments

ps	Phyloseq file
title	Title for NMDS plots
env_parameters	Environment parameters to use for the envfit
classifying_parameters	Parameters used to color and shape the samples points - Unquoted
sample_color	Parameter used to color the samples (e.g. fraction_name) - Unquoted
sample_shape	Parameter used for shape of the samples (e.g. season) - Unquoted
sample_label	Parameter used to label the samples (e.g. sample_label) - Unquoted
taxo_level	Taxonomic level to color the OTUs (e.g. division) - Unquoted
taxo_colors	Colors to be used to color the OTUs Plot the bargraph Returns a list made of 2 elements (ggplots) gg_samples = samples with env parameters as ggplot gg_taxa = taxa colored

Examples

print(phyloseq_long_asv_bargraph(phyloseq_nmds, title= "Antartica")

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