Professional Comprehensive Omics Data Analysis

Documentation for package ‘pctax’ version 0.1.7

Help Pages

-- 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

-- K --

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 --

-- S --

-- 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 plot for difference analysis

-- Z --

z_diversity	Calculate Zeta Diversity
z_diversity_decay	Calculate Zeta Diversity with Distance