tsg_ind: Transform data from wide to long, without aggregating...

In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Description

Transform data from wide to long, without aggregating individual samples.

Usage

tsg_ind(
  df,
  n = 50,
  ar_mean = FALSE,
  geo_mean = FALSE,
  otu_ord = NULL,
  tax_df = otu_good_taxonomy,
  tax_level = NULL,
  sample_col = "Sample_name"
)

Arguments

df	Dataframe containing metadata and taxon (Phylum, Otu, etc) abundance data in wide format.
n	Number of OTUs to return, 50 by default.
ar_mean	Boolean to indicate whether the arithmetic mean should be appended to the data.
geo_mean	Boolean to indicate whether the geometric mean should be appended to the data.
otu_ord	Character or factor vector of unique OTU identifiers. These are often ordered OTUs resulting from taxon_sort_gather and are used to ensure consistency in OTU ordering and factor levels across dataframes.
tax_df	Taxonomy table. Passed to join_tax. Defaults to otu_good_taxonomy.
tax_level	Taxonomic level(s) to join from tax_df. Defaults to NULL, in which case no join occurs.
sample_col	Single element character vector specifying the column in df which contains Sample names. Defaults to Sample_name.

Value

An unaggregated dataframe that has been reshaped into long form.

See Also

taxon_sort_gather

Examples

mock_gg <- dplyr::filter(otu_df, Experiment == "Zymo_Mock") %>%
    tsg_ind(n = 20, ar_mean = T, geo_mean = T)

filt_df_ind <- dplyr::filter(otu_df, Experiment %in% c("A", "B"),
    Treatment_group == "TG1", Organ == "Feces", Day == 11) %>%
    tsg_ind(otu_ord = levels(filt_df$OTU))

cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.