Setup
Load packages. tidyverse is a collection of useful packages for data science.
# install.packages("pak")
# pak::pak("tidyverse")
library(conflicted) # for safety
library(tidyverse)
library(ranemone)Set options for your data and cache directories. See the Get started page for details.
Reading files
Read all files with the given file name recursively in
directory_prefix().
sample_df = ranemone::read_tsv_xz("sample.tsv.xz")
experiment_df = ranemone::read_tsv_xz("experiment.tsv.xz")
community_df = ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz")Using community tables
The community table contains many columns. You may want to select a smaller number of columns for analysis.
dim(community_df)
str(community_df)
comm = community_df |>
dplyr::select(samplename, family, genus, species, sequence, nreads, ncopiesperml)
dim(comm)
str(comm)
print(comm)Taxonomy of available species can be extracted with a single function.
taxonomy = community_df |> ranemone::distinct_taxonomy()Alpha diversity can be calculated using the ncopiesperml
column after aggregating them for each species in each sample.
species_df = community_df |>
ranemone::summarize_ncopies(.by = species)
dim(species_df)
str(species_df)
print(species_df)
diversity = ranemone::summarize_alpha_diversity(species_df)You can replace species with genus,
family, or other levels as needed.
Making community composition tables
A community composition matrix in wider format is also supported.
species_mat = community_df |>
ranemone::pivot_wider_ncopies(.by = species)
ranemone::calc_alpha_div(species_mat)