I have written several custom functions to expedite some of the functions that I reuse multiple times for data sets across different sample and taxon subsets. The loop below will use one of those functions to read the microeco datasets that I built using the MicroEcoDataPrep script.
This code makes use of the dataset paths referenced in my config.yaml file. To see the full path (relative to the repository base directory), refer to the relative syntax in this script and the config file below.
default:
setup: "setup/global/setup.R"
knit_engines: "setup/global/knit_engines.R"
conflicts: "setup/global/conflicts.R"
functions: "setup/global/functions.R"
packages: "setup/global/packages.R"
inputs: "setup/global/inputs.R"
fonts: "setup/global/fonts/FA6_Free-Solid-900.otf"
test_prediction: "setup/microbiome/test_prediction/"
visuals: "visuals/"
summaries:
metadata: "../summaries/metadata/"
tmp_tsv: "tmp/tmp_table.tsv"
tmp_downloads: "tmp/downloads/"
tmp_fetch: "tmp/fetch_references.txt"
tmp_fasta3: "tmp/tmp3.fasta"
tmp_fasta4: "tmp/tmp4.fasta"
modules:
generate_alignment_stats: "modules/generate_alignment_stats.R"
reactable_functions: "modules/reactable_functions.R"
reactable_columns: "modules/reactable_columns.R"
microbiome:
micro_scripts: !expr list("setup/microbiome/packages.R", "setup/microbiome/functions.R", "setup/microbiome/inputs.R")
setup_dir: "setup/microbiome"
inputs: "setup/microbiome/inputs.R"
packages: "setup/microbiome/packages.R"
first_use_packages: "setup/microbiome/packages_first_use.R"
functions: "setup/microbiome/functions.R"
tax4fun: "setup/microbiome/Tax4Fun2_ReferenceData_v2/"
Ref99NR: "setup/microbiome/Tax4Fun2_ReferenceData_v2/Ref99NR/"
blast: "setup/microbiome/ncbi-blast-2.16.0+/bin"
swan:
functions: "setup/read_processing/functions.R"
loris_tax: "/work/richlab/aliciarich/bioinformatics_stats/data/loris/taxonomy/"
uid_file: "/work/richlab/aliciarich/bioinformatics_stats/tmp/fetch_references.txt"
logs: "/work/richlab/aliciarich/bioinformatics_stats/logs"
ont_reads: "/work/richlab/aliciarich/ont_reads/"
dorado_model: "/work/richlab/aliciarich/ont_reads/dna_r10.4.1_e8.2_400bps_sup@v5.0.0/"
bioinformatics_stats: "/work/richlab/aliciarich/bioinformatics_stats"
samplesheets: "/work/richlab/aliciarich/bioinformatics_stats/dataframes/sample_sheet/loris"
scripts: "/work/richlab/aliciarich/bioinformatics_stats/batch_scripts/"
accessions: "/work/richlab/aliciarich/bioinformatics_stats/tmp/accessions.txt"
tmp_fasta1: "/work/richlab/aliciarich/bioinformatics_stats/tmp/tmp1.fasta"
tmp_fasta2: "/work/richlab/aliciarich/bioinformatics_stats/tmp/tmp2.fasta"
tmp_fasta3: "/work/richlab/aliciarich/bioinformatics_stats/tmp/tmp3.fasta"
tmp_fasta4: "/work/richlab/aliciarich/bioinformatics_stats/tmp/tmp4.fasta"
raw_loris_mb: "/work/richlab/aliciarich/ont_reads/loris_microbiome/hdz_raw"
basecalled_loris_mb: "/work/richlab/aliciarich/ont_reads/loris_microbiome/basecalled"
trimmed_loris_mb: "/work/richlab/aliciarich/ont_reads/loris_microbiome/trimmed"
filtered_loris_mb: "/work/richlab/aliciarich/ont_reads/loris_microbiome/filtered"
loris_mb_aligned: "/work/richlab/aliciarich/bioinformatics_stats/data/loris/taxonomy/refseqs_aligned.fasta"
loris_mb_tree: "/work/richlab/aliciarich/bioinformatics_stats/data/loris/taxonomy/refseqs_tree.newick"
loris:
day1: "2023-10-26"
last: "2024-10-25"
sequencing:
coverage: "visuals/loris_depth_summary.html"
depth_plot: "visuals/loris_depth_hist.html"
metadata:
scripts: !expr list("metadata/loris/colors.R", "metadata/loris/metadata_key.R", "metadata/loris/nutrition.R", "metadata/loris/hdz_loris_log.R", "metadata/loris/diet_tables.R")
bristol: "metadata/loris/bristols.tsv"
studbook: "metadata/loris/subjects_loris.csv"
summary: "metadata/loris/samples_metadata.tsv"
key: "metadata/loris/metadata_key.R"
factors: "metadata/loris/factors.R"
foods: "metadata/loris/foods.tsv"
proteins: "metadata/loris/proteins.tsv"
fats: "metadata/loris/fats.tsv"
CHOs: "metadata/loris/CHOs.tsv"
Ash: "metadata/loris/Ash.tsv"
vitamins: "metadata/loris/vitamins.tsv"
reactable: "metadata/loris/loris_metadata_summary.html"
inventories:
all_stages: "dataframes/sample_inventories/compilation_loris.tsv"
collection: "dataframes/sample_inventories/samples_loris.csv"
extraction: "dataframes/sample_inventories/extracts_loris.csv"
libraries: "dataframes/sample_inventories/libraries_loris.csv"
seqruns: "dataframes/sample_inventories/seqruns_loris.csv"
outputs_wf16s: "data/loris/outputs_wf16s/"
barcodes_output: "dataframes/barcodes/loris/"
read_alignments: "data/loris/read_alignments"
taxa_reps:
aligned: "data/loris/taxonomy/refseqs_aligned.fasta"
tree: "data/loris/taxonomy/refseqs_tree.newick"
table: "data/loris/taxonomy/tax_table.tsv"
abundance_wf16s: "data/loris/wf16s_abundance/"
microeco:
dataset:
main:
kegg: "microeco/loris/datasets/main/keg_dataset_main"
njc: "microeco/loris/datasets/main/njc_dataset_main"
fpt: "microeco/loris/datasets/main/fpt_dataset_main"
phylum: "microeco/loris/datasets/main/phy_dataset_main"
class: "microeco/loris/datasets/main/cla_dataset_main"
order: "microeco/loris/datasets/main/ord_dataset_main"
family: "microeco/loris/datasets/main/fam_dataset_main"
genus: "microeco/loris/datasets/main/gen_dataset_main"
species: "microeco/loris/datasets/main/spe_dataset_main"
culi:
kegg: "microeco/loris/datasets/culi/keg_dataset_culi"
njc: "microeco/loris/datasets/culi/njc_dataset_culi"
fpt: "microeco/loris/datasets/culi/fpt_dataset_culi"
phylum: "microeco/loris/datasets/culi/phy_dataset_culi"
class: "microeco/loris/datasets/culi/cla_dataset_culi"
order: "microeco/loris/datasets/culi/ord_dataset_culi"
family: "microeco/loris/datasets/culi/fam_dataset_culi"
genus: "microeco/loris/datasets/culi/gen_dataset_culi"
species: "microeco/loris/datasets/culi/spe_dataset_culi"
warb:
kegg: "microeco/loris/datasets/warble/keg_dataset_warb"
njc: "microeco/loris/datasets/warble/njc_dataset_warb"
fpt: "microeco/loris/datasets/warble/fpt_dataset_warb"
phylum: "microeco/loris/datasets/warble/phy_dataset_warb"
class: "microeco/loris/datasets/warble/cla_dataset_warb"
order: "microeco/loris/datasets/warble/ord_dataset_warb"
family: "microeco/loris/datasets/warble/fam_dataset_warb"
genus: "microeco/loris/datasets/warble/gen_dataset_warb"
species: "microeco/loris/datasets/warble/spe_dataset_warb"
abund:
main:
kegg: "microeco/loris/abundance/main/keg_abund_main"
fpt: "microeco/loris/abundance/main/fpt_abund_main"
njc: "microeco/loris/abundance/main/njc_abund_main"
phylum: "microeco/loris/abundance/main/phy_abund_main/Phylum_abund.tsv"
class: "microeco/loris/abundance/main/cla_abund_main/Class_abund.tsv"
order: "microeco/loris/abundance/main/ord_abund_main/Order_abund.tsv"
family: "microeco/loris/abundance/main/fam_abund_main/Family_abund.tsv"
genus: "microeco/loris/abundance/main/gen_abund_main/Genus_abund.tsv"
species: "microeco/loris/abundance/main/spe_abund_main/Species_abund.tsv"
culi:
kegg: "microeco/loris/abundance/culi/keg_abund_culi"
fpt: "microeco/loris/abundance/culi/fpt_abund_culi"
njc: "microeco/loris/abundance/culi/njc_abund_culi"
phylum: "microeco/loris/abundance/culi/phy_abund_culi/Phylum_abund.tsv"
class: "microeco/loris/abundance/culi/cla_abund_culi/Class_abund.tsv"
order: "microeco/loris/abundance/culi/ord_abund_culi/Order_abund.tsv"
family: "microeco/loris/abundance/culi/fam_abund_culi/Family_abund.tsv"
genus: "microeco/loris/abundance/culi/gen_abund_culi/Genus_abund.tsv"
species: "microeco/loris/abundance/culi/spe_abund_culi/Species_abund.tsv"
warb:
kegg: "microeco/loris/abundance/warble/keg_abund_warb"
fpt: "microeco/loris/abundance/warble/fpt_abund_warb"
njc: "microeco/loris/abundance/warble/njc_abund_warb"
phylum: "microeco/loris/abundance/warble/phy_abund_warb/Phylum_abund.tsv"
class: "microeco/loris/abundance/warble/cla_abund_warb/Class_abund.tsv"
order: "microeco/loris/abundance/warble/ord_abund_warb/Order_abund.tsv"
family: "microeco/loris/abundance/warble/fam_abund_warb/Family_abund.tsv"
genus: "microeco/loris/abundance/warble/gen_abund_warb/Genus_abund.tsv"
species: "microeco/loris/abundance/warble/spe_abund_warb/Species_abund.tsv"
alpha:
main:
kegg: "microeco/loris/alphadiversity/main/keg_alphadiv_main"
fpt: "microeco/loris/alphadiversity/main/fpt_alphadiv_main"
njc: "microeco/loris/alphadiversity/main/njc_alphadiv_main"
phylum: "microeco/loris/alphadiversity/main/phy_alphadiv_main/alpha_diversity.csv"
class: "microeco/loris/alphadiversity/main/cla_alphadiv_main/alpha_diversity.csv"
order: "microeco/loris/alphadiversity/main/ord_alphadiv_main/alpha_diversity.csv"
family: "microeco/loris/alphadiversity/main/fam_alphadiv_main/alpha_diversity.csv"
genus: "microeco/loris/alphadiversity/main/gen_alphadiv_main/alpha_diversity.csv"
species: "microeco/loris/alphadiversity/main/spe_alphadiv_main/alpha_diversity.csv"
culi:
kegg: "microeco/loris/alphadiversity/culi/keg_alphadiv_culi"
fpt: "microeco/loris/alphadiversity/culi/fpt_alphadiv_culi"
njc: "microeco/loris/alphadiversity/culi/njc_alphadiv_culi"
phylum: "microeco/loris/alphadiversity/culi/phy_alphadiv_culi/alpha_diversity.csv"
class: "microeco/loris/alphadiversity/culi/cla_alphadiv_culi/alpha_diversity.csv"
order: "microeco/loris/alphadiversity/culi/ord_alphadiv_culi/alpha_diversity.csv"
family: "microeco/loris/alphadiversity/culi/fam_alphadiv_culi/alpha_diversity.csv"
genus: "microeco/loris/alphadiversity/culi/gen_alphadiv_culi/alpha_diversity.csv"
species: "microeco/loris/alphadiversity/culi/spe_alphadiv_culi/alpha_diversity.csv"
warb:
kegg: "microeco/loris/alphadiversity/warble/keg_alphadiv_warb"
fpt: "microeco/loris/alphadiversity/warble/fpt_alphadiv_warb"
njc: "microeco/loris/alphadiversity/warble/njc_alphadiv_warb"
phylum: "microeco/loris/alphadiversity/warble/phy_alphadiv_warb/alpha_diversity.csv"
class: "microeco/loris/alphadiversity/warble/cla_alphadiv_warb/alpha_diversity.csv"
order: "microeco/loris/alphadiversity/warble/ord_alphadiv_warb/alpha_diversity.csv"
family: "microeco/loris/alphadiversity/warble/fam_alphadiv_warb/alpha_diversity.csv"
genus: "microeco/loris/alphadiversity/warble/gen_alphadiv_warb/alpha_diversity.csv"
species: "microeco/loris/alphadiversity/warble/spe_alphadiv_warb/alpha_diversity.csv"
beta:
main:
kegg: "microeco/loris/betadiversity/main/keg_betadiv_main"
fpt: "microeco/loris/betadiversity/main/fpt_betadiv_main"
njc: "microeco/loris/betadiversity/main/njc_betadiv_main"
phylum:
aitchison: "microeco/loris/betadiversity/main/phy_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/phy_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/phy_betadiv_main/wei_unifrac.csv"
class:
aitchison: "microeco/loris/betadiversity/main/cla_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/cla_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/cla_betadiv_main/wei_unifrac.csv"
order:
aitchison: "microeco/loris/betadiversity/main/ord_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/ord_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/ord_betadiv_main/wei_unifrac.csv"
family:
aitchison: "microeco/loris/betadiversity/main/fam_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/fam_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/fam_betadiv_main/wei_unifrac.csv"
genus:
aitchison: "microeco/loris/betadiversity/main/gen_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/gen_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/gen_betadiv_main/wei_unifrac.csv"
species:
aitchison: "microeco/loris/betadiversity/main/spe_betadiv_main/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/main/spe_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/main/spe_betadiv_main/wei_unifrac.csv"
culi:
kegg: "microeco/loris/betadiversity/culi/keg_betadiv_culi"
fpt: "microeco/loris/betadiversity/culi/fpt_betadiv_culi"
njc: "microeco/loris/betadiversity/culi/njc_betadiv_culi"
phylum:
aitchison: "microeco/loris/betadiversity/culi/phy_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/phy_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/phy_betadiv_culi/wei_unifrac.csv"
class:
aitchison: "microeco/loris/betadiversity/culi/cla_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/cla_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/cla_betadiv_culi/wei_unifrac.csv"
order:
aitchison: "microeco/loris/betadiversity/culi/ord_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/ord_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/ord_betadiv_culi/wei_unifrac.csv"
family:
aitchison: "microeco/loris/betadiversity/culi/fam_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/fam_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/fam_betadiv_culi/wei_unifrac.csv"
genus:
aitchison: "microeco/loris/betadiversity/culi/gen_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/gen_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/gen_betadiv_culi/wei_unifrac.csv"
species:
aitchison: "microeco/loris/betadiversity/culi/spe_betadiv_culi/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/culi/spe_betadiv_culi/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/culi/spe_betadiv_culi/wei_unifrac.csv"
warb:
kegg: "microeco/loris/betadiversity/warble/keg_betadiv_warb"
fpt: "microeco/loris/betadiversity/warble/fpt_betadiv_warb"
njc: "microeco/loris/betadiversity/warble/njc_betadiv_warb"
phylum:
aitchison: "microeco/loris/betadiversity/warb/phy_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/phy_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/phy_betadiv_warb/wei_unifrac.csv"
class:
aitchison: "microeco/loris/betadiversity/warb/cla_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/cla_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/cla_betadiv_warb/wei_unifrac.csv"
order:
aitchison: "microeco/loris/betadiversity/warb/ord_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/ord_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/ord_betadiv_warb/wei_unifrac.csv"
family:
aitchison: "microeco/loris/betadiversity/warb/fam_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/fam_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/fam_betadiv_warb/wei_unifrac.csv"
genus:
aitchison: "microeco/loris/betadiversity/warb/gen_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/gen_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/gen_betadiv_warb/wei_unifrac.csv"
species:
aitchison: "microeco/loris/betadiversity/warb/spe_betadiv_warb/aitchison.csv"
unifrac_u: "microeco/loris/betadiversity/warb/spe_betadiv_warb/unwei_unifrac.csv"
unifrac_w: "microeco/loris/betadiversity/warb/spe_betadiv_warb/wei_unifrac.csv"
data:
main:
phylum:
feature: "microeco/loris/datasets/main/phy_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/phy_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/phy_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/phy_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/phy_dataset_main/tax_table.tsv"
class:
feature: "microeco/loris/datasets/main/cla_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/cla_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/cla_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/cla_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/cla_dataset_main/tax_table.tsv"
order:
feature: "microeco/loris/datasets/main/ord_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/ord_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/ord_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/ord_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/ord_dataset_main/tax_table.tsv"
family:
feature: "microeco/loris/datasets/main/fam_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/fam_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/fam_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/fam_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/fam_dataset_main/tax_table.tsv"
genus:
feature: "microeco/loris/datasets/main/gen_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/gen_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/gen_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/gen_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/gen_dataset_main/tax_table.tsv"
species:
feature: "microeco/loris/datasets/main/spe_dataset_main/feature_table.tsv"
tree: "microeco/loris/datasets/main/spe_dataset_main/phylo_tree.tre"
fasta: "microeco/loris/datasets/main/spe_dataset_main/rep_fasta.fasta"
samples: "microeco/loris/datasets/main/spe_dataset_main/sample_table.tsv"
taxa: "microeco/loris/datasets/main/spe_dataset_main/tax_table.tsv"
culi:
phylum:
feature: "microeco/loris/datasets/culi/phy_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/phy_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/phy_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/phy_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/phy_dataset_culi/tax_table.tsv"
class:
feature: "microeco/loris/datasets/culi/cla_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/cla_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/cla_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/cla_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/cla_dataset_culi/tax_table.tsv"
order:
feature: "microeco/loris/datasets/culi/ord_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/ord_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/ord_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/ord_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/ord_dataset_culi/tax_table.tsv"
family:
feature: "microeco/loris/datasets/culi/fam_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/fam_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/fam_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/fam_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/fam_dataset_culi/tax_table.tsv"
genus:
feature: "microeco/loris/datasets/culi/gen_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/gen_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/gen_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/gen_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/gen_dataset_culi/tax_table.tsv"
species:
feature: "microeco/loris/datasets/culi/spe_dataset_culi/feature_table.tsv"
tree: "microeco/loris/datasets/culi/spe_dataset_culi/phylo_tree.tre"
fasta: "microeco/loris/datasets/culi/spe_dataset_culi/rep_fasta.fasta"
samples: "microeco/loris/datasets/culi/spe_dataset_culi/sample_table.tsv"
taxa: "microeco/loris/datasets/culi/spe_dataset_culi/tax_table.tsv"
warb:
phylum:
feature: "microeco/loris/datasets/warb/phy_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/phy_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/phy_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/phy_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/phy_dataset_warb/tax_table.tsv"
class:
feature: "microeco/loris/datasets/warb/cla_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/cla_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/cla_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/cla_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/cla_dataset_warb/tax_table.tsv"
order:
feature: "microeco/loris/datasets/warb/ord_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/ord_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/ord_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/ord_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/ord_dataset_warb/tax_table.tsv"
family:
feature: "microeco/loris/datasets/warb/fam_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/fam_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/fam_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/fam_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/fam_dataset_warb/tax_table.tsv"
genus:
feature: "microeco/loris/datasets/warb/gen_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/gen_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/gen_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/gen_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/gen_dataset_warb/tax_table.tsv"
species:
feature: "microeco/loris/datasets/warb/spe_dataset_warb/feature_table.tsv"
tree: "microeco/loris/datasets/warb/spe_dataset_warb/phylo_tree.tre"
fasta: "microeco/loris/datasets/warb/spe_dataset_warb/rep_fasta.fasta"
samples: "microeco/loris/datasets/warb/spe_dataset_warb/sample_table.tsv"
taxa: "microeco/loris/datasets/warb/spe_dataset_warb/tax_table.tsv"
marmoset:
extracts: "dataframes/sample_inventories/extracts_marmoset.tsv"
libraries: "dataframes/sample_inventories/libraries_marmoset.tsv"
samples: "dataframes/sample_inventories/samples_marmoset.tsv"
compilation: "dataframes/sample_inventories/compilation_marmoset.tsv"
libraries_csv: "../data/libraries_marmoset.csv"
seqruns_csv: "../data/seqruns_marmoset.csv"
compilation_csv: "../data/compilation_marmoset.csv"
extracts_csv: "../data/extracts_marmoset.csv"
samples_csv: "../data/samples_marmoset.csv"
barcodes_output: "dataframes/barcodes/marmoset/"
barcode_alignments: "../labwork/minion_data/barcode_alignments/marmoset/"
sample_sheet: "marmoset/dataframes/sample_sheet/"
taxonomy_list: "marmoset/dataframes/taxonomy_list/"
microeco:
abund:
main:
phylum: "microeco/marmoset/abundance/main/phy_abund_main/Phylum_abund.tsv"
class: "microeco/marmoset/abundance/main/cla_abund_main/Class_abund.tsv"
order: "microeco/marmoset/abundance/main/ord_abund_main/Order_abund.tsv"
family: "microeco/marmoset/abundance/main/fam_abund_main/Family_abund.tsv"
genus: "microeco/marmoset/abundance/main/gen_abund_main/Genus_abund.tsv"
species: "microeco/marmoset/abundance/main/spe_abund_main/Species_abund.tsv"
bysubj:
phylum: "microeco/marmoset/abundance/bysubject/phylum/"
class: "microeco/marmoset/abundance/bysubject/class/"
order: "microeco/marmoset/abundance/bysubject/order/"
family: "microeco/marmoset/abundance/bysubject/family/"
genus: "microeco/marmoset/abundance/bysubject/genus/"
species: "microeco/marmoset/abundance/bysubject/species/"
alpha:
main:
phylum: "microeco/marmoset/alphadiversity/main/phy_alphadiv_main/alpha_diversity.csv"
class: "microeco/marmoset/alphadiversity/main/cla_alphadiv_main/alpha_diversity.csv"
order: "microeco/marmoset/alphadiversity/main/ord_alphadiv_main/alpha_diversity.csv"
family: "microeco/marmoset/alphadiversity/main/fam_alphadiv_main/alpha_diversity.csv"
genus: "microeco/marmoset/alphadiversity/main/gen_alphadiv_main/alpha_diversity.csv"
species: "microeco/marmoset/alphadiversity/main/spe_alphadiv_main/alpha_diversity.csv"
bysubj:
phylum: "microeco/marmoset/alphadiversity/bysubject/phylum/"
class: "microeco/marmoset/alphadiversity/bysubject/class/"
order: "microeco/marmoset/alphadiversity/bysubject/order/"
family: "microeco/marmoset/alphadiversity/bysubject/family/"
genus: "microeco/marmoset/alphadiversity/bysubject/genus/"
species: "microeco/marmoset/alphadiversity/bysubject/species/"
beta:
main:
phylum:
canber: "microeco/marmoset/betadiversity/main/phy_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/phy_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/phy_betadiv_main/wei_unifrac.csv"
class:
canber: "microeco/marmoset/betadiversity/main/cla_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/cla_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/cla_betadiv_main/wei_unifrac.csv"
order:
canber: "microeco/marmoset/betadiversity/main/ord_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/ord_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/ord_betadiv_main/wei_unifrac.csv"
family:
canber: "microeco/marmoset/betadiversity/main/fam_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/fam_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/fam_betadiv_main/wei_unifrac.csv"
genus:
canber: "microeco/marmoset/betadiversity/main/gen_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/gen_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/gen_betadiv_main/wei_unifrac.csv"
species:
canber: "microeco/marmoset/betadiversity/main/spe_betadiv_main/canberra.csv"
unifrac_u: "microeco/marmoset/betadiversity/main/spe_betadiv_main/unwei_unifrac.csv"
unifrac_w: "microeco/marmoset/betadiversity/main/spe_betadiv_main/wei_unifrac.csv"
bysubj:
phylum: "microeco/marmoset/betadiversity/bysubject/phylum/"
class: "microeco/marmoset/betadiversity/bysubject/class/"
order: "microeco/marmoset/betadiversity/bysubject/order/"
family: "microeco/marmoset/betadiversity/bysubject/family/"
genus: "microeco/marmoset/betadiversity/bysubject/genus/"
species: "microeco/marmoset/betadiversity/bysubject/species/"
data:
main:
phylum:
feature: "microeco/marmoset/datasets/main/phy_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/phy_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/phy_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/phy_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/phy_dataset_main/tax_table.tsv"
class:
feature: "microeco/marmoset/datasets/main/cla_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/cla_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/cla_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/cla_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/cla_dataset_main/tax_table.tsv"
order:
feature: "microeco/marmoset/datasets/main/ord_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/ord_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/ord_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/ord_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/ord_dataset_main/tax_table.tsv"
family:
feature: "microeco/marmoset/datasets/main/fam_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/fam_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/fam_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/fam_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/fam_dataset_main/tax_table.tsv"
genus:
feature: "microeco/marmoset/datasets/main/gen_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/gen_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/gen_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/gen_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/gen_dataset_main/tax_table.tsv"
species:
feature: "microeco/marmoset/datasets/main/spe_dataset_main/feature_table.tsv"
tree: "microeco/marmoset/datasets/main/spe_dataset_main/phylo_tree.tre"
fasta: "microeco/marmoset/datasets/main/spe_dataset_main/rep_fasta.fasta"
samples: "microeco/marmoset/datasets/main/spe_dataset_main/sample_table.tsv"
taxa: "microeco/marmoset/datasets/main/spe_dataset_main/tax_table.tsv"
bysubj:
phylum: "microeco/marmoset/datasets/bysubject/phylum/"
class: "microeco/marmoset/datasets/bysubject/class/"
order: "microeco/marmoset/datasets/bysubject/order/"
family: "microeco/marmoset/datasets/bysubject/family/"
genus: "microeco/marmoset/datasets/bysubject/genus/"
species: "microeco/marmoset/datasets/bysubject/species/"
bats:
extracts: "dataframes/sample_inventories/extracts_bats.tsv"
libraries: "dataframes/sample_inventories/libraries_bats.tsv"
samples: "dataframes/sample_inventories/samples_bats.tsv"
compilation: "dataframes/sample_inventories/compilation_bats.tsv"
compilation_csv: "../data/compilation_bats.csv"
extracts_csv: "../data/extracts_bats.csv"
samples_csv: "../data/samples_bats.csv"
isolates:
extracts: "dataframes/sample_inventories/extracts_isolates.tsv"
libraries: "dataframes/sample_inventories/libraries_isolates.tsv"
samples: ".../bioinformatics_stats/dataframes/sample_inventories/samples_isolates.tsv"
compilation: "dataframes/sample_inventories/compilation_isolates.tsv"
compilation_csv: "../data/compilation_isolates.csv"
extracts_csv: "../data/extracts_isolates.csv"
samples_csv: "../data/samples_isolates.csv"
envir:
extracts: "dataframes/sample_inventories/extracts_envir.tsv"
libraries: "dataframes/sample_inventories/libraries_envir.tsv"
samples: "dataframes/sample_inventories/samples_envir.tsv"
compilation: "dataframes/sample_inventories/compilation_envir.tsv"
compilation_csv: "../data/compilation_envir.csv"
extracts_csv: "../data/extracts_envir.csv"
samples_csv: "../data/samples_envir.csv"
sample_sheets:
compilations:
loris: "dataframes/sample_sheet/loris/hdz_combined_sample_sheet.csv"
marmoset: "dataframes/sample_sheet/marmoset/cm_combined_sample_sheet.csv"
hdz1: "dataframes/sample_sheet/loris/hdz1_sample_sheet.csv"
hdz2: "dataframes/sample_sheet/loris/hdz2_sample_sheet.csv"
hdz3: "dataframes/sample_sheet/loris/hdz3_sample_sheet.csv"
hdz4: "dataframes/sample_sheet/loris/hdz4_sample_sheet.csv"
hdz5: "dataframes/sample_sheet/loris/hdz5_sample_sheet.csv"
hdz6: "dataframes/sample_sheet/loris/hdz6_sample_sheet.csv"
hdz7: "dataframes/sample_sheet/loris/hdz7_sample_sheet.csv"
hdz8: "dataframes/sample_sheet/loris/hdz8_sample_sheet.csv"
hdz9: "dataframes/sample_sheet/loris/hdz9_sample_sheet.csv"
hdz10: "dataframes/sample_sheet/loris/hdz10_sample_sheet.csv"
hdz11: "dataframes/sample_sheet/loris/hdz11_sample_sheet.csv"
hdz12: "dataframes/sample_sheet/loris/hdz12_sample_sheet.csv"
hdz13: "dataframes/sample_sheet/loris/hdz13_sample_sheet.csv"
hdz14: "dataframes/sample_sheet/loris/hdz14_sample_sheet.csv"
hdz15: "dataframes/sample_sheet/loris/hdz15_sample_sheet.csv"
hdz16: "dataframes/sample_sheet/loris/hdz16_sample_sheet.csv"
hdz17: "dataframes/sample_sheet/loris/hdz17_sample_sheet.csv"
hdz18: "dataframes/sample_sheet/loris/hdz18_sample_sheet.csv"
cm001: "dataframes/sample_sheet/marmoset/cm001_sample_sheet.csv"
cm002: "dataframes/sample_sheet/marmoset/cm002_sample_sheet.csv"
cm003: "dataframes/sample_sheet/marmoset/cm003_sample_sheet.csv"
cm004: "dataframes/sample_sheet/marmoset/cm004_sample_sheet.csv"
cm005: "dataframes/sample_sheet/marmoset/cm005_sample_sheet.csv"
cm006: "dataframes/sample_sheet/marmoset/cm006_sample_sheet.csv"
cm007: "dataframes/sample_sheet/marmoset/cm007_sample_sheet.csv"
cm008: "dataframes/sample_sheet/marmoset/cm008_sample_sheet.csv"
cm009: "dataframes/sample_sheet/marmoset/cm009_sample_sheet.csv"
cm010: "dataframes/sample_sheet/marmoset/cm010_sample_sheet.csv"
cm011: "dataframes/sample_sheet/marmoset/cm011_sample_sheet.csv"
barcode_alignments:
compilations:
loris: "../labwork/minion_data/barcode_alignments/loris/hdz_combined_barcode_alignment.tsv"
marmoset: "../labwork/minion_data/barcode_alignments/marmoset/cm_combined_barcode_alignment.tsv"
hdz1: "../labwork/minion_data/barcode_alignments/loris/hdz1_barcode_alignment.tsv"
hdz2: "../labwork/minion_data/barcode_alignments/loris/hdz2_barcode_alignment.tsv"
hdz3: "../labwork/minion_data/barcode_alignments/loris/hdz3_barcode_alignment.tsv"
hdz4: "../labwork/minion_data/barcode_alignments/loris/hdz4_barcode_alignment.tsv"
hdz5: "../labwork/minion_data/barcode_alignments/loris/hdz5_barcode_alignment.tsv"
hdz6: "../labwork/minion_data/barcode_alignments/loris/hdz6_barcode_alignment.tsv"
hdz7: "../labwork/minion_data/barcode_alignments/loris/hdz7_barcode_alignment.tsv"
hdz8: "../labwork/minion_data/barcode_alignments/loris/hdz8_barcode_alignment.tsv"
hdz9: "../labwork/minion_data/barcode_alignments/loris/hdz9_barcode_alignment.tsv"
hdz10: "../labwork/minion_data/barcode_alignments/loris/hdz10_barcode_alignment.tsv"
hdz11: "../labwork/minion_data/barcode_alignments/loris/hdz11_barcode_alignment.tsv"
hdz12: "../labwork/minion_data/barcode_alignments/loris/hdz12_barcode_alignment.tsv"
hdz13: "../labwork/minion_data/barcode_alignments/loris/hdz13_barcode_alignment.tsv"
hdz14: "../labwork/minion_data/barcode_alignments/loris/hdz14_barcode_alignment.tsv"
hdz15: "../labwork/minion_data/barcode_alignments/loris/hdz15_barcode_alignment.tsv"
hdz16: "../labwork/minion_data/barcode_alignments/loris/hdz16_barcode_alignment.tsv"
hdz17: "../labwork/minion_data/barcode_alignments/loris/hdz17_barcode_alignment.tsv"
hdz18: "../labwork/minion_data/barcode_alignments/loris/hdz18_barcode_alignment.tsv"
cm001: "../labwork/minion_data/barcode_alignments/marmoset/cm001_barcode_alignment.tsv"
cm002: "../labwork/minion_data/barcode_alignments/marmoset/cm002_barcode_alignment.tsv"
cm003: "../labwork/minion_data/barcode_alignments/marmoset/cm003_barcode_alignment.tsv"
cm004: "../labwork/minion_data/barcode_alignments/marmoset/cm004_barcode_alignment.tsv"
cm005: "../labwork/minion_data/barcode_alignments/marmoset/cm005_barcode_alignment.tsv"
cm006: "../labwork/minion_data/barcode_alignments/marmoset/cm006_barcode_alignment.tsv"
cm007: "../labwork/minion_data/barcode_alignments/marmoset/cm007_barcode_alignment.tsv"
cm008: "../labwork/minion_data/barcode_alignments/marmoset/cm008_barcode_alignment.tsv"
cm009: "../labwork/minion_data/barcode_alignments/marmoset/cm009_barcode_alignment.tsv"
cm010: "../labwork/minion_data/barcode_alignments/marmoset/cm010_barcode_alignment.tsv"
cm011: "../labwork/minion_data/barcode_alignments/marmoset/cm011_barcode_alignment.tsv"
abund_wf16s_files:
hdz1: "data/loris/wf16s_abundance/hdz1_abundance_table_species.tsv"
hdz2: "data/loris/wf16s_abundance/hdz2_abundance_table_species.tsv"
hdz3: "data/loris/wf16s_abundance/hdz3_abundance_table_species.tsv"
hdz4: "data/loris/wf16s_abundance/hdz4_abundance_table_species.tsv"
hdz5: "data/loris/wf16s_abundance/hdz5_abundance_table_species.tsv"
hdz6: "data/loris/wf16s_abundance/hdz6_abundance_table_species.tsv"
hdz7: "data/loris/wf16s_abundance/hdz7_abundance_table_species.tsv"
hdz8: "data/loris/wf16s_abundance/hdz8_abundance_table_species.tsv"
hdz9: "data/loris/wf16s_abundance/hdz9_abundance_table_species.tsv"
hdz10: "data/loris/wf16s_abundance/hdz10_abundance_table_species.tsv"
hdz11: "data/loris/wf16s_abundance/hdz11_abundance_table_species.tsv"
hdz12: "data/loris/wf16s_abundance/hdz12_abundance_table_species.tsv"
hdz13: "data/loris/wf16s_abundance/hdz13_abundance_table_species.tsv"
hdz14: "data/loris/wf16s_abundance/hdz14_abundance_table_species.tsv"
hdz15: "data/loris/wf16s_abundance/hdz15_abundance_table_species.tsv"
hdz16: "data/loris/wf16s_abundance/hdz16_abundance_table_species.tsv"
hdz17: "data/loris/wf16s_abundance/hdz17_abundance_table_species.tsv"
hdz18: "data/loris/wf16s_abundance/hdz18_abundance_table_species.tsv"
cm001: "data/marmoset/wf16s_abundance/cm001_abundance_table_species.tsv"
cm002: "data/marmoset/wf16s_abundance/cm002_abundance_table_species.tsv"
cm003: "data/marmoset/wf16s_abundance/cm003_abundance_table_species.tsv"
cm004: "data/marmoset/wf16s_abundance/cm004_abundance_table_species.tsv"
cm005: "data/marmoset/wf16s_abundance/cm005_abundance_table_species.tsv"
cm006: "data/marmoset/wf16s_abundance/cm006_abundance_table_species.tsv"
cm007: "data/marmoset/wf16s_abundance/cm007_abundance_table_species.tsv"
cm008: "data/marmoset/wf16s_abundance/cm008_abundance_table_species.tsv"
cm009: "data/marmoset/wf16s_abundance/cm009_abundance_table_species.tsv"
cm010: "data/marmoset/wf16s_abundance/cm010_abundance_table_species.tsv"
cm011: "data/marmoset/wf16s_abundance/cm011_abundance_table_species.tsv"
methods_16s:
libprep_workflow: "'rapid16s'"
dorado_model: "'dna_r10.4.1_e8.2_400bps_sup@v5.0.0'"
min_length: 1000
max_length: 2000
min_qual: 7
min_id: 85
min_cov: 80
kit_name: "'SQK-16S114-24'"
tax_rank: "S"
n_taxa_barplot: 12
abund_threshold: 0
loris:
rarefy: 4500
norm: "SRS"
min_abund: 0.0001
min_freq: 0.02
inlcude_lowest: TRUE
unifrac: TRUE
betadiv: "aitchison"
alpha_pd: TRUE
tax4fun_db: "Ref99NR"
loris_rarefy: 4500
keg_minID: 97
loris_norm: "SRS"
loris_filter:
rel_abund: 0.0001
freq: 0.02
inlcude_lowest: TRUE
notebooks:
AMR: "../Notebooks/Rich/"
SA: "../Notebooks/Azadmanesh/"
TA: "../Notebooks/Raad/"
TSP: "../Notebooks/Palacio/"
DG: "../Notebooks/Gill/"
# Define dataset categories
dataset_types <- c("tax", "function")
tax_levels <- c("species", "genus", "family", "order", "class", "phylum")
func_levels <- c("kegg", "fpt", "njc")
datasets <- c("main", "culi", "warb")
# Create an empty list to store all datasets
microtable_datasets <- list()
# Helper function to safely read files
safe_read <- function(file, ...) {
if (file.exists(file)) {
return(read.table(file, ...))
} else {
warning(paste("File missing:", file))
return(NULL)
}
}
# Loop through dataset types (taxonomic and functional)
for (data_type in dataset_types) {
levels <- if (data_type == "tax") tax_levels else func_levels
for (level in levels) {
for (dataset in datasets) {
# Extract dataset path from config
if (!is.null(dataset_dir[[dataset]][[level]])) {
directory <- dataset_dir[[dataset]][[level]]
} else {
warning(paste("Path not found in config for:", dataset, level))
next # Skip this iteration if the path is missing
}
# Generate dataset name
prefix <- substr(level, 1, 3) # Extract first 3 letters
dataset_name <- paste0(prefix, ".dataset.", dataset)
# Read required files
sample_tab <- safe_read(file.path(directory, "sample_table.tsv") , sep = "\t", header = TRUE, row.names = 1)
tax_table <- safe_read(file.path(directory, "tax_table.tsv") , sep = "\t", header = TRUE, row.names = 1)
otu_table <- safe_read(file.path(directory, "feature_table.tsv"), sep = "\t", header = TRUE, row.names = 1)
# Create dataset object
if (data_type == "tax") {
phylo_tree <- if (file.exists(file.path(directory,
"phylo_tree.tre"))) read.tree(file.path(directory,
"phylo_tree.tre")) else NULL
rep_fasta <- if (file.exists(file.path(directory,
"rep_fasta.fasta"))) read.fasta(file.path(directory,
"rep_fasta.fasta")) else NULL
microtable_datasets[[dataset_name]] <- microtable$new(
sample_table = sample_tab,
otu_table = otu_table,
tax_table = tax_table,
phylo_tree = phylo_tree,
rep_fasta = rep_fasta,
auto_tidy = TRUE
)
} else {
microtable_datasets[[dataset_name]] <- microtable$new(
sample_table = sample_tab,
otu_table = otu_table,
tax_table = tax_table,
auto_tidy = TRUE
)
}
}
}
}
# Convert list to global environment variables if needed
list2env(microtable_datasets, envir = .GlobalEnv)<environment: R_GlobalEnv>