# Professional Comprehensive Omics Data Analysis

## Documentation for package ‘pctax’ version 0.1.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G I K L M N P R S T V Z

## -- A --

add_strip | add strips for a tree plot
add_tax | Add taxonomy for a pc_otu object
ALDEX | ALDEX
all_ec_info | all element cycle information.
all_sp_la_zh_name | all species latin names and chinese names
ann_tree | Annotate a tree
aor | Calculate Abundance-occupancy_relationship
aor.data.frame | Calculate Abundance-occupancy_relationship
as.b_dist | Transfer dist to b_dist
as.dist.b_dist | Transfer b_dist to dist
a_diversity | Calculate a_diversity of otutab
a_diversity.data.frame | Calculate a_diversity of otutab
a_diversity.numeric | Calculate a_diversity of otutab
a_diversity.pc_otu | Calculate a_diversity of otutab

## -- B --

batch_mediate | Batch mediate
bbtt | ggdotchart for diff analysis
before_tree | Before df2tree check
b_analyse | Beta_diversity Ordination: dimensionality reduction
b_analyse.data.frame | Beta_diversity Ordination: dimensionality reduction
b_NTI1 | Calculate beta_NTI
b_res_3d | 3D plot for b_res

## -- C --

check_taxonkit | Check taxonkit
convert_taxon_name | Convert taxon names between Chinese and Latin
cor_net | Correlation network, species-interaction network for omics

## -- D --

df2tree | From a dataframe to construct a phylo
df2tree1 | From a dataframe to construct a phylo (save nwk)
diff_da | Difference analysis
download_taxonkit_dataset | Download taxonkit dataset
drop_tips_update | Drop Tips and Update a Phylogenetic Tree

## -- E --

easy_tree | Annotate a tree
envfitt | Envfit test for RDA result

## -- G --

geo_sim | Lm for sample similarity and geographical distance
get_all_sp_la_zh_name | get all species Latin and Chinese name from the CCTCC database
get_diff_type | Get mean and type
gp_dis_density | Group inter-intra density
grap_p_test | Performs graph-based permutation tests

## -- I --

install_taxonkit | Install taxonkit

## -- K --

kwtest | KW test

## -- L --

load_mpa_df | Load a metaphlan format data.frame
load_N_data | Load N-cycle data

## -- M --

mat_dist | Calculate distance for otutab
micro_sbatch | Microbiome sbatch
multi_bar | Difference analysis
multi_conf | Difference analysis
myCAP | RDA
myCCA | RDA
mydbRDA | RDA
myRDA | RDA

## -- N --

name_or_id2df | Transfer taxon name or taxid to the lineage dataframe
ncm | Sloan Neutral Model
nst | Calculate NST for each group
nti_rc | Calculate b_NTI and RC_bray for each group

## -- P --

pc_otu | Create a pc_otu class object
pc_tax1 | test data (pc_otu class) for pc_tax package.
pc_valid | Judge pc_otu is valid or not
permanova | Permanova between a otutab and a variable
plot.AOR | Calculate Abundance-occupancy_relationship
plot.a_res | Plot a_res object
plot.b_dist | Transfer dist to b_dist
plot.b_res | Plot a b_res
plot.dist | Transfer dist to b_dist
plot.g_test | Plot g_test
plot.ncm_res | Sloan Neutral Model
plot.NTI_RC | Calculate b_NTI and RC_bray for each group
plot.pro_res | Plot pro_res
plot.rare_res | Rare the sample
plot.time_cm | Plot time_cm
plot.zeta_decay | Calculate Zeta Diversity with Distance
plot.zeta_res | Calculate Zeta Diversity
plot_checkm2_res | Visualize CheckM2 Genome Quality Assessment Results
plot_contigs_quality | Visualize Contigs Quality Metrics
plot_element_cycle | Plot element cycle
plot_gtdb_tr | Plot GTDB-Tk Phylogenetic Tree with Taxonomic Coloring
plot_N_cycle | Plot the N-cycling pathway and genes
plot_one_phage | Plot Individual Phage Genome Structure with Annotations
plot_two_tree | Plot two trees in one plot
pre_assembly_stats | Prepare the result from assembly_stats (.json file)
pre_fastp | Prepare the result from fastp (.json file)
pre_format_report | Preprocess MPA Species Abundance and Taxonomy Data
pre_genomad | Preprocess geNomad and CheckV Output Results
pre_gtdb_tk | Preprocess GTDB-Tk Classification Results
pre_tax_table | Complete a taxonomy table
print.pc_otu | Print
print.virus_res | Print method for virus_res objects
procrustes_analyse | Procrustes Rotation of Two Configurations and PROTEST

## -- R --

rarefaction | Rarefy a otutab
rare_curve_sample | Rare the sample
rare_curve_species | Rare the species
RCbray1 | Calculate RCbray-curtis
RDA_plot | Plot RDA res

## -- S --

stamp_plot | Stamp style plot
suijisenlin | RandomForest
summary.pc_otu | Summary pc_otu

## -- T --

taxonkit_filter | Filter TaxIDs based on Taxonomic Ranks
taxonkit_lca | Compute Lowest Common Ancestor (LCA) of TaxIDs
taxonkit_lineage | Retrieve Taxonomic Lineage using taxonkit
taxonkit_list | Taxonkit list
taxonkit_name2taxid | Convert Taxonomic Names to TaxIDs
taxonkit_reformat | Reformat Taxonomic Lineage using taxonkit
tax_lca | Calculate the lowest common ancestor (LCA) of a set of taxa
time_by_cm | Time series analysis

## -- V --

volcano_p | Volcano plot for difference analysis

## -- Z --

z_diversity | Calculate Zeta Diversity
z_diversity_decay | Calculate Zeta Diversity with Distance