Professional Comprehensive Omics Data Analysis

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Documentation for package ‘pctax’ version 0.1.1

• 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.
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
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_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
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
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