ngsLCA R package

ngsLCA R package provides functionality for processing lca files generated by the ngsLCA main program and illustrating the taxonomic profiles.

Installation

Install the released version of ngsLCA from CRAN with:

install.packages("ngsLCA")

Install the released version of ngsLCA from github with:

remotes::install_github("wyc661217/ngsLCA")

or:

devtools::install_github("wyc661217/ngsLCA")

Example workflow

Running ngsLCA R package (and this workflow) requires all lca files to be processed being placed in a folder as input, with each input lca file normally representing a sample. This example workflow will run through all ngsLCA R functions. The output files and results will be generated into “Desktop/project_files/lca_files/run03”.

Define work directory and name of the run:

library(ngsLCA)

working_directory="Desktop/project_files/lca_files/" #change it to the path of your lca files folder.
run_name="run03"

Generate a complete taxa profile by combining all input lca files (this step is required for running all other functions):

ngsLCA_profile(path=working_directory,
               run=run_name,
               metadata="Desktop/project_files/sample_metadata.txt") #change it to the full path of your sample metadata.

Filter the combined taxa profile:

ngsLCA_filter(path=working_directory,
              run=run_name,
              remove.taxa="1115501,10114", #taxa ID indicate taxa that will be removed from the results.
              threshold.1=2,
              threshold.2=0,
              threshold.3=5)

De-contaminate the combined taxa profile:

ngsLCA_deContam(path=working_directory,
                run=run_name,
                control_path="Desktop/project_files/blank_control_lca_files/", #change it to the full path of your blank control lca files folder.
                threshold.1_control=2,
                threshold.2_control=0,
                threshold.3_control=5)

Group taxa into user-defined taxa groups:

ngsLCA_group(path=working_directory,
             run=run_name,
             group.name="Viruses,Archaea,Bacteria,Fungi,Viridiplantae,Metazoa",
             threshold.perGroup=0)

Classify taxa to taxonomic ranks:

ngsLCA_rank(path=working_directory,
            run=run_name,
            rank.name="species,genus,family")

Count reads and taxa numbers:

ngsLCA_count(path=working_directory,
             run=run_name)

Generate files that can be inputted into Megan for taxa profiling:

ngsLCA_meganFile(path=working_directory,
                 run=run_name)

Generate taxa abundance heatmaps:

ngsLCA_heatmap(path=working_directory,
               run=run_name,
               taxa.number=30)

Generate taxa abundance barplots:

ngsLCA_barplot(path=working_directory,
               run=run_name,
               taxa.number=20)

Perform rarefaction on taxa reads abundance:

ngsLCA_rarefy(path=working_directory,
              run=run_name)

Perform taxa profiles NMDS:

ngsLCA_NMDS(path=working_directory,
            run=run_name,
            dimension=2,
            trymax=10)

Generate taxa abundance stratplots:

ngsLCA_stratplot(path=working_directory,
                 run=run_name,
                 taxa.number=20)