# pctax

`pctax` provides a comprehensive suite of tools for analyzing omics data.

## Vignette

Please go to https://bookdown.org/Asa12138/pctax_book/ for the full vignette.

## Install

    install.packages("devtools")
    devtools::install_github("Asa12138/pcutils")
    devtools::install_github("Asa12138/pctax")

## Usage

It includes functionalities for α-diversity analysis, β-diversity analysis, differential abundance analysis, community assembly, visualization of phylogenetic tree and functional enrichment analysis…

Look at the test data:

    library(pctax)
    library(pcutils)
    data(otutab, package = "pcutils")
    # help(otutab)

    head(otutab)
    #>                               NS1  NS2  NS3  NS4  NS5  NS6  WS1  WS2  WS3  WS4
    #> s__un_f__Thermomonosporaceae 1092 1920  810 1354 1064 1070 1252 1597 1330  941
    #> s__Pelomonas_puraquae        1962 1234 2362 2236 2903 1829  644  495 1230 1284
    #> s__Rhizobacter_bergeniae      588  458  889  901 1226  853  604  470 1070 1028
    #> s__Flavobacterium_terrae      244  234 1810  673 1445  491  318 1926 1493  995
    #> s__un_g__Rhizobacter         1432  412  533  759 1289  506  503  590  445  620
    #> s__un_o__Burkholderiales      886  683  824  912 1502 1029  235  252  359  381
    #>                               WS5  WS6  CS1  CS2  CS3  CS4  CS5  CS6
    #> s__un_f__Thermomonosporaceae 1233 1011 2313 2518 1709 1975 1431 1527
    #> s__Pelomonas_puraquae         953  635 1305 1516  844 1128 1483 1174
    #> s__Rhizobacter_bergeniae      846  670 1029 1802 1002 1200 1194  762
    #> s__Flavobacterium_terrae      577  359 1080 1218  754  423 1032 1412
    #> s__un_g__Rhizobacter          657  429 1132 1447  550  583 1105  903
    #> s__un_o__Burkholderiales      387  351  551  540  477  559  513  496
    head(metadata)
    #>      Id Group     env1     env2     env3      env4     env5        env6
    #> NS1 NS1    NS 3.057248 10.23571 5.554576  8.084997 25.00795 -1.15456682
    #> NS2 NS2    NS 4.830219 11.13453 5.613455  8.556829 16.67690  0.81168745
    #> NS3 NS3    NS 3.753133 10.06232 5.582916 10.226572 21.68926  1.40733211
    #> NS4 NS4    NS 4.262264 10.84401 5.258419  9.002256 24.81046  1.47805320
    #> NS5 NS5    NS 2.476135  7.52584 6.255314  9.357587 19.70553  0.05813095
    #> NS6 NS6    NS 5.131004 10.82761 5.180966  8.141506 18.39021 -1.70032569
    #>          lat     long
    #> NS1 26.94422 103.4767
    #> NS2 29.08733 109.6196
    #> NS3 28.25164 104.0361
    #> NS4 33.82415 106.8651
    #> NS5 33.51011 105.4571
    #> NS6 31.86864 102.7832
    head(taxonomy)
    #>                                  Kingdom            Phylum
    #> s__un_f__Thermomonosporaceae k__Bacteria p__Actinobacteria
    #> s__Pelomonas_puraquae        k__Bacteria p__Proteobacteria
    #> s__Rhizobacter_bergeniae     k__Bacteria p__Proteobacteria
    #> s__Flavobacterium_terrae     k__Bacteria  p__Bacteroidetes
    #> s__un_g__Rhizobacter         k__Bacteria p__Proteobacteria
    #> s__un_o__Burkholderiales     k__Bacteria p__Proteobacteria
    #>                                               Class               Order
    #> s__un_f__Thermomonosporaceae      c__Actinobacteria  o__Actinomycetales
    #> s__Pelomonas_puraquae         c__Betaproteobacteria  o__Burkholderiales
    #> s__Rhizobacter_bergeniae     c__Gammaproteobacteria  o__Pseudomonadales
    #> s__Flavobacterium_terrae          c__Flavobacteriia o__Flavobacteriales
    #> s__un_g__Rhizobacter         c__Gammaproteobacteria  o__Pseudomonadales
    #> s__un_o__Burkholderiales      c__Betaproteobacteria  o__Burkholderiales
    #>                                                Family
    #> s__un_f__Thermomonosporaceae   f__Thermomonosporaceae
    #> s__Pelomonas_puraquae               f__Comamonadaceae
    #> s__Rhizobacter_bergeniae          f__Pseudomonadaceae
    #> s__Flavobacterium_terrae         f__Flavobacteriaceae
    #> s__un_g__Rhizobacter              f__Pseudomonadaceae
    #> s__un_o__Burkholderiales     f__un_o__Burkholderiales
    #>                                                     Genus
    #> s__un_f__Thermomonosporaceae g__un_f__Thermomonosporaceae
    #> s__Pelomonas_puraquae                        g__Pelomonas
    #> s__Rhizobacter_bergeniae                   g__Rhizobacter
    #> s__Flavobacterium_terrae                g__Flavobacterium
    #> s__un_g__Rhizobacter                       g__Rhizobacter
    #> s__un_o__Burkholderiales         g__un_o__Burkholderiales
    #>                                                   Species
    #> s__un_f__Thermomonosporaceae s__un_f__Thermomonosporaceae
    #> s__Pelomonas_puraquae               s__Pelomonas_puraquae
    #> s__Rhizobacter_bergeniae         s__Rhizobacter_bergeniae
    #> s__Flavobacterium_terrae         s__Flavobacterium_terrae
    #> s__un_g__Rhizobacter                 s__un_g__Rhizobacter
    #> s__un_o__Burkholderiales         s__un_o__Burkholderiales

## Citation

Please cite:

Chen Peng (2023). pctax: Professional Comprehensive Omics Data Analysis. R package, https://github.com/Asa12138/pctax.