reorder_samples_by: Reorder the samples or stacked group levels by abundance

In KarstensLab/microshades: A custom color palette for improving data visualization

Reorder the samples or stacked group levels by abundance

Description

This function will reorder the user selected subgroup taxa based on abundance, and can also reorder the stacked groups levels based on abundance, using sink_abundant_groups

Usage

reorder_samples_by(
  mdf_group,
  cdf,
  order_tax = "NA",
  group_level = "Phylum",
  subgroup_level = "Genus",
  sample_variable = "Sample",
  sample_ordering = NA,
  sink_abundant_groups = TRUE
)

Arguments

mdf_group	data.frame, data frame containing microbiome data
cdf	data.frame containing the color key
group_level	string of larger taxonomic group
subgroup_level	string of smaller taxonomic group
sample_variable	sample variable to reorder (x- axis component for plot)
sample_ordering	list of samples in desired order for plotting
sink_abundant_groups	logical reorder the phylum groups so the most abundant is the bottom group
order	string of subgroup to reorder by

Value

list

• "mdf" reordered melted data frame, ready for plotting

• "cdf" reordered manual color filling according to new order

Examples

library(phyloseq)
data(GlobalPatterns)

mdf <- prep_mdf(GlobalPatterns)

color_obj <- create_color_dfs(mdf)

mdf_group <- color_obj$mdf
cdf <- color_obj$cdf

mdf_new <- reorder_samples_by(mdf_group, cdf)
mdf_new <- reorder_samples_by(mdf_group, cdf, order_tax = "Bacteroides")

KarstensLab/microshades documentation built on June 11, 2024, 11:41 a.m.