create_color_dfs: Generates abundance sorted data frame and a color palette...

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

Generates abundance sorted data frame and a color palette data frame

Description

Use create_color_dfs() to create a specialized data frames containing color and abundance organized microbiome data.

Usage

create_color_dfs(
  mdf,
  selected_groups = c("Proteobacteria", "Actinobacteria", "Bacteroidetes", "Firmicutes"),
  top_n_subgroups = 4,
  group_level = "Phylum",
  subgroup_level = "Genus",
  cvd = FALSE,
  top_orientation = FALSE
)

Arguments

mdf	data.frame, melted data frame containing microbiome data
selected_groups	list of groups in group_level taxomomy to specify and color in plot. The vector order is the stacking order. "Other" is always on the top of the stack, but then the rest will follow. The default is "Proteobacteria", "Actinobacteria", "Bacteroidetes", "Firmicutes". "Firmicutes" is on the bottom of the stack.
top_n_subgroups	integer number of top subgroups to show for each selected group the max is 4 top subgroups
group_level	string of larger taxonomic group
subgroup_level	string of smaller taxonomic group
cvd	logical, determines which palette to use, color vision deficent (microshades_cvd_palettes) or microshades_palettes
top_orientation	logical most abundant shades oriented at the top of the stack otherwise, most abundant shades are bottom oriented

Details

The top group categories are user specified through the selected_groups parameter, and top subgroup categories are dynamically generated based on abundance. For the top group, the categories not in selected_groups will be changed to "Other". The top_n_subgroups will be determined for each selected group.

Notes:

• In SILVA 138, some phylum names are different and you should consider passing in the vector c("Proteobacteria", "Actinobacteriota", "Bacteroidota", "Firmicutes")

Value

list

• "mdf" melted data frame to pass into ggplot2

• "cdf" mapping to be used in manual color filling

Examples

library(phyloseq)
data(GlobalPatterns)

mdf <- prep_mdf(GlobalPatterns)

colorframe <- create_color_dfs(mdf)
colorframe <- create_color_dfs(mdf, selected_groups = c("Proteobacteria", "Actinobacteriota", "Bacteroidota", "Firmicutes"))
colorframe <- create_color_dfs(mdf, cvd = TRUE)

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