# Professional Comprehensive Omics Data Analysis

## Documentation for package ‘pctax’ version 0.1.3

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

## Help Pages

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
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
check_taxonkit | Check taxonkit
convert_taxon_name | Convert taxon names between Chinese and Latin
cor_net | Correlation network, species-interaction network for omics
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
easy_tree | Annotate a tree
envfitt | Envfit test for RDA result
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
install_taxonkit | Install taxonkit
kwtest | KW test
load_N_data | Load N-cycle data
mat_dist | Calculate distance for otutab
micro_sbatch | Microbiome sbatch
multi_bar | Difference analysis
myCAP | RDA
myCCA | RDA
myRDA | RDA
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
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_element_cycle | Plot element cycle
plot_N_cycle | Plot the N-cycling pathway and genes
plot_two_tree | Plot two trees in one plot
pre_fastp | Prepare the result from fastp (.json file)
pre_tax_table | Complete a taxonomy table
print.pc_otu | Print
procrustes_analyse | Procrustes Rotation of Two Configurations and PROTEST
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
suijisenlin | RandomForest
summary.pc_otu | Summary pc_otu
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
volcano_p | Volcano plot for difference analysis
z_diversity | Calculate Zeta Diversity
z_diversity_decay | Calculate Zeta Diversity with Distance