#' @title Microbiome analysis pipeline
#' @description Function microbiome_pipeline generates an HTML report with preliminary QC, Alpha Diversity, Ordination and
#' Composition analysis of OTU tables. This function save all intermediate files incuding figures and phyloseq
#' objects in user specified directory.
#' @param otufile biom object, otu_table in csv format or mothur shared files.
#' @param mapping Metadata variable to check for groups based sequencing effort csv format.
#' @param taxonomy NULL or csv fomatted file.
#' @param treefilename for phylogenetic based diversity analysis "*.tre" file
#' @param type "biom", "mothur", "simple" simple is for *.csv file.
#' @param work_dir Working directory where input files are stored.
#' @param out_dir Output directory where all outputs are to be stored.
#' @param VariableA Main variable of interest.
#' @param VariableB Secondary variable of interest.
#' @param UnConstOrd If unconstrained ordination to be plotted TRUE or FALSE.
#' @param heatmap Heatmap or not option is TRUE or FALSE.
#' @param filterCount Filter OTUs below this count number.
#' @param filterPrev Filter OTUs not detected in less than this percent of samples.
#' @param col.palette = 'Spectral', 'Set2', 'Paired' use any of the RColorbrewer palette depending on number of groups
#' you have in VaraibleA.
#' @param filterpseq TRUE or FALSE.
#' @param samsize Number of reads to rarefy your data and save the rarefied phyobject.
#' @param projectname Name of the project.
#' @param author Name of the author/investigator.
#' @author Contact: Sudarshan Shetty \email{sudarshanshetty9@@gmail.com}
#' @return A HTML report with graphs and data stats.
#' @import tidyr
#' @import dplyr
#' @import microbiome
#' @import phyloseq
#' @import ggplot2
#' @export
#' @examples \dontrun{
#'
#' library(microbiomeutilities)
#' library(microbiome)
#' microbiome_pipeline(otufile = "my.biom",
#' mapping = "mymap.csv",
#' taxonomy = NULL,
#' treefilename = "myTree.tre",
#' type = "biom",
#' work_dir = "F:/path/my/input/filefolder",
#' out_dir = "F:/path/to/save/my/files/folder",
#' VariableA = "MC_type1",
#' VariableB = "Region",
#' UnConstOrd = TRUE,
#' heatmap = TRUE,
#' filterCount = 4,
#' filterPrev = 0.01,
#' col.palette = "Paired",
#' filterpseq = TRUE,
#' samsize = NA,
#' projectname = "Mock",
#' author = "Sudarshan")
#' }
#' @keywords utilities
microbiome_pipeline <- function(otufile,
mapping,
taxonomy,
treefilename,
type,
work_dir,
out_dir,
VariableA,
VariableB,
UnConstOrd,
heatmap,
filterCount,
filterPrev,
col.palette,
filterpseq,
samsize,
projectname,
author){
{
rmarkdown::render(input=system.file("microutility_template.rmd", package="microbiomeutilities"),
output_file=paste0(projectname, "_report.html"),
output_dir=work_dir,
knit_root_dir=work_dir,
run_pandoc=TRUE,
quiet=FALSE,
clean=TRUE,
params = list(
otufile,
mapping,
taxonomy,
treefilename,
type,
work_dir,
out_dir,
VariableA,
VariableB,
UnConstOrd,
heatmap,
filterCount,
filterPrev,
col.palette,
filterpseq,
samsize,
projectname,
author))
cat("HTML report created in output directory\n")
}
}
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