Title: Schloss Lab Tools for Reproducible Microbiome Research
Version: 0.4.1
Date: 2023-08-21
Description: A collection of useful functions and example code created and used by the Schloss Lab for reproducible microbiome research. Perform common tasks like read files created by mothur https://mothur.org/, tidy up your microbiome data, and format R Markdown documents for publication. See the website http://www.schlosslab.org/schtools/ for more information, documentation, and examples.
License: MIT + file LICENSE
URL: http://www.schlosslab.org/schtools/, https://github.com/SchlossLab/schtools
BugReports: https://github.com/SchlossLab/schtools/issues
Imports: dplyr, formatR, glue, rlang, stringr, tidyr
Suggests: covr, cowplot, ggplot2, ggtext, here, hexSticker, hrbrthemes, knitr, purrr, readr, rmarkdown, showtext, testthat
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2023-08-21 13:53:26 UTC; sovacool
Author: Kelly Sovacool ORCID iD [aut, cre], Nicholas Lesniak ORCID iD [aut], Sarah Lucas ORCID iD [aut], Courtney Armour ORCID iD [aut], Patrick Schloss [aut], Jacqueline Moltzau ORCID iD [ctb], Andrew Hannah [ctb], Nielson Baxter [ctb], Alyxandria Schubert [ctb], Kathryn Iverson [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Repository: CRAN
Date/Publication: 2023-08-21 14:50:06 UTC

schtools: Schloss Lab Tools for Reproducible Microbiome Research

Description

A collection of useful functions and example code created and used by the Schloss Lab for reproducible microbiome research. Perform common tasks like read files created by mothur, tidy up your microbiome data, and format rmarkdown documents for publication. See the website for more information, documentation, and examples.

Author(s)

Maintainer: Kelly Sovacool sovacool@umich.edu (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Calculate OTU relative abundances from a shared file

Description

Calculate OTU relative abundances from a shared file

Usage

calc_relabun(abs_abun_dat)

Arguments

abs_abun_dat

a data frame from reading in a shared file. Should contain a Group column for sample names, Otu columns for absolute counts of each OTU, and rows as each sample.

Value

a new data frame with OTU relative abundances in long format.

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples

shared_dat <- readr::read_tsv(system.file("extdata", "test.shared",
  package = "schtools"
))
shared_dat %>% calc_relabun()

Check whether two numeric vectors are close enough

Description

This is like dplyr::near() except with much less precision.

Usage

close_enough(x, y, tol = 10^-3)

Arguments

x

a numeric vector

y

another numeric vector

tol

tolerance (default: 10^-3.)

Value

TRUE if all numbers are near enough within the tolerance, otherwise FALSE

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples


close_enough(0.0004, 0)
close_enough(0.8887, 0.8884)
close_enough(1, 2)

Format human-readable numbers.

Description

Pastes formatted x if numeric, otherwise x unmodified. Circumvents R's automatic scientific notation. If a number is nearly whole (see is_nearly_whole()), it is rounded to have zero decimal places. Otherwise, numbers >= 1 are rounded to 1 decimal place; numbers < 1 are rounded to have 2 significant digits.

Usage

format_number(x, nsmall = 1, signif_precise = 2)

Arguments

x

inline code

nsmall

number of digits after the decimal point to round to when x is not nearly whole but x >= 1.

signif_precise

number of significant digits to use when x is not nearly whole

Value

formatted x if numeric, otherwise x unmodified.

Author(s)

Pat Schloss pschloss@umich.edu

Kelly Sovacool sovacool@umich.edu

Examples

format_number(0.0256)
format_number(.Machine$double.eps^0.5)
format_number(100000.08)
format_number(1.00000000000000000001)
format_number("this is a string")

Get the Snakemake wildcards as a tibble

Description

Get the Snakemake wildcards as a tibble

Usage

get_wildcards_tbl()

Value

a tibble of wildcards, with columns as names and rows as values

Author(s)

Kelly Sovacool sovacool@umich.edu

Inline hook for knitr to paste human-readable numbers and nice lists.

Description

Inline hook for knitr to paste human-readable numbers and nice lists.

Usage

inline_hook(x)

Arguments

x

just about anything

Value

a string where each element in x is separated by a comma and numbers are in a human-readable format.

Author(s)

Kelly Sovacool sovacool@umich.edu

Pat Schloss pschloss@umich.edu

Examples

inline_hook(c(1.2993992, 0.03, 1000))
inline_hook(c("cats", "dogs"))

Checks whether a number is near to a whole number

Description

Checks whether a number is near to a whole number

Usage

is_nearly_whole(x)

Arguments

x

a numeric

Value

TRUE or FALSE

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples

is_nearly_whole(.Machine$double.eps^0.5)
is_nearly_whole(.Machine$double.eps^0.6)
is_nearly_whole(1)

Check whether all elements given are sorted in non-descending order

Description

Check whether all elements given are sorted in non-descending order

Usage

is_nondesc(...)

Arguments

...

anything!

Value

TRUE if the elements are sorted in non-descending order, otherwise FALSE

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples


is_nondesc(1, 2, 3)
is_nondesc(c(1, 2), 3)
is_nondesc(6, 4, 1)
is_nondesc("a", "b", "c")
is_nondesc(c("z", "y"))

Install & load packages

Description

Install & load packages

Usage

load_deps(...)

Arguments

...

package names to install & load

Author(s)

Kelly Sovacool sovacool@umich.edu

Save output, messages, warnings, and errors to the Snakemake log file

Description

This function checks whether a log file was specified in the Snakemake rule. If so, it directs any output, messages, warnings, or errors to the rule-specific log file. See the Snakemake documentation on log files and R scripts for more details.

Usage

log_snakemake(quiet = TRUE)

Arguments

quiet

Silence messages about the status of the snakemake object and log file (default: TRUE).

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples

# The Snakemake object doesn't exist, so nothing happens
log_snakemake(quiet = FALSE)

Convert taxonomy strings into dataframe of labels based on taxonomic classification

Description

Convert taxonomy strings into dataframe of labels based on taxonomic classification

Usage

parse_tax(dat)

Arguments

dat

dataframe from mothur taxonomy file with columns OTU, Size, and Taxonomy

Value

a wide dataframe with taxonomic labels

Author(s)

Nick Lesniak, nlesniak@umich.edu

Examples

taxonomy_filepath <- system.file("extdata",
  "test.taxonomy",
  package = "schtools"
)
taxonomy_tbl <- read_tax(taxonomy_filepath)
head(taxonomy_tbl)

Create a prose string from a list or vector

Description

The word 'and' is inserted before the last element and an Oxford comma is used.

Usage

paste_oxford_list(x)

Arguments

x

a list or vector

Value

a string where each element in x is separated by a comma

Author(s)

Pat Schloss pschloss@umich.edu

Kelly Sovacool sovacool@umich.edu

Examples

paste_oxford_list(1:3)
paste_oxford_list(c("cats", "dogs", "turtles"))

Pool OTU counts at a particular taxonomic level

Description

Enables comparing analyses at different taxonomic resolutions, as seen in doi:10.1128/mbio.03161-21. Implementation adapted from here.

Usage

pool_taxon_counts(otu_shared_dat, otu_tax_dat, taxon_level)

Arguments

otu_shared_dat

data frame created from a shared file at the OTU level.

otu_tax_dat

data frame created from a taxonomy file at the OTU level. Must be from the same dataset as the shared file.

taxon_level

taxonomic level to pool OTUs into. Options: "kingdom", "phylum", "class", "order", "family", "genus". This should be the name of a column in otu_tax_dat as a character string.

Value

a shared data frame with the OTUs at the specified taxon_level and a corresponding taxonomy dataframe with new OTU numbers.

Author(s)

Kelly Sovacool, sovacool@umich.edu

Pat Schloss pschloss@umich.edu

Examples

tax_dat <- read_tax(system.file("extdata", "test.taxonomy",
  package = "schtools"
))
shared_dat <- readr::read_tsv(system.file("extdata", "test.shared",
  package = "schtools"
))
pool_taxon_counts(shared_dat, tax_dat, "genus")
pool_taxon_counts(shared_dat, tax_dat, "family")
pool_taxon_counts(shared_dat, tax_dat, "phylum")

Read in lower left triangular matrix from file

Description

Read in lower left triangular matrix from file

Usage

read_dist(dist_filename)

Arguments

dist_filename

filename of lower left triangular matrix (.dist)

Value

distance matrix as a tibble

Author(s)

Nick Lesniak, nlesniak@umich.edu

Examples

dist_filepath <- system.file("extdata",
  "sample.final.thetayc.0.03.lt.ave.dist",
  package = "schtools"
)
dist_tbl <- read_dist(dist_filepath)
head(dist_tbl)

Read in a taxonomy file and parse it to a wide dataframe

Description

Read in a taxonomy file and parse it to a wide dataframe

Usage

read_tax(taxonomy_filename, sep = "\t")

Arguments

taxonomy_filename

filename of taxonomy file

sep

Character that separates fields of the taxonomy file. (Default: ⁠\t⁠).

Value

dataframe of taxonomic labels, formatted by parse_tax()

Author(s)

Nick Lesniak, nlesniak@umich.edu

Kelly Sovacool, sovacool@umich.edu

Examples

taxonomy_filepath <- system.file("extdata",
  "test.taxonomy",
  package = "schtools"
)
taxonomy_tbl <- read_tax(taxonomy_filepath)
head(taxonomy_tbl)

dplyr pipe

Description

These objects are imported from other packages. Follow the links below to see their documentation.

dplyr

%>%

rlang

.data

Set knitr chunk options & inline hook

Description

Call this function in the setup chunk of your R Markdown files.

Usage

set_knitr_opts()

Author(s)

Pat Schloss pschloss@umich.edu

Kelly Sovacool sovacool@umich.edu

Sarah's go-to theme for ggplot2

Description

Requires the hrbrthemes package and the ⁠PT Sans⁠ and ⁠PT Sans Narrow⁠ fonts from Google Fonts.

Usage

theme_lucas()

Value

list of ggproto objects

Author(s)

Sarah Lucas salucas@umich.edu

Examples

library(ggplot2)
library(showtext)

# run once to download the PT Sans fonts
font_add_google(name = "PT Sans", family = "PT Sans")
font_add_google(name = "PT Sans Narrow", family = "PT Sans Narrow")
showtext_auto()

# make a plot with theme_lucas()
ggplot(mtcars) +
  aes(x = mpg, y = wt, color = cyl) +
  geom_point() +
  theme_lucas()

Kelly's go-to theme for ggplot2

Description

Uses ggplot2::theme_bw() and removes margins.

Usage

theme_sovacool()

Value

list of ggproto objects

Author(s)

Kelly Sovacool sovacool@umich.edu

Examples

library(ggplot2)
ggplot(mtcars) +
  aes(x = mpg, y = wt, color = cyl) +
  geom_point() +
  theme_sovacool()