makebargraphrawggplot2: ggplot2-based cummulative stacked bargraphs for plotting...
In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

Description Usage Arguments Value Examples

This function uses a taxonomy file (i.e. an RDP naive bayesian fixed-rank asignment detail) and a shared file to create 100 Only the top-n OTUs (in relative abundance) among all samples are displayed. All other OTUs are summed into a part of the graph designated as "other". The resulting object contains information about the composition of "other".

makebargraphrawggplot2(
  tax,
  shared,
  topn = 8,
  taxlevel = c("Regnum", "Phylum", "Classis", "Ordo", "Familia", "Genus", "Species"),
  shared.abs = T,
  tax.prob = F,
  tresh = 85,
  samples,
  viridfill = FALSE,
  plot = TRUE,
  ...
)

`tax`	is a taxonomy file, raw.
`shared`	is a shared (OTU-by-sample) file, filtered per sample group.
`topn`	is the top number of taxa selected to display (maximum 11, default 8)
`taxlevel`	is either one of "Regnum", "Phylum", "Classis", "Ordo", "Familia", "Genus"
`shared.abs`	is a logical showing wether the shared file already consists out of direct Illumina counts, or is really the raw csv from Ramiro (default TRUE)
`tax.prob`	shows whether the taxonomy file contains probabilites (default FALSE)
`tresh`	is a threshold for the probability taxonomy duplicate matching (to be implemented, default 85)
`samples`	is an optional string for the title of the generated bargraph (e.g. "MOB","OLAND","Fecal samples", defualt empty)
`viridfill`	whether or not a discrete viridis fill pallette should be used (defaults to FALSE)
`plot`	states wether or not to print the plot within the function (default TRUE)
`...`	optional arguments passed on to ggplot call

a list of 3 objects: ggplotdf (the underlying data for the ggplot), othertax (an abundance-sorted dataframe of the OTUs summarized in "other"), ggplotobj (the generated ggplot2 object)

## Short example
# make sure library(CMETNGS) is loaded
shareddataset <- system.file("extdata","large_shared_file.shared",
                              package = "CMETNGS",mustWork = TRUE)
taxonomydataset <- system.file("extdata","large_OTU_basedtax.taxonomy",
                              package = "CMETNGS",mustWork = TRUE)

shared <- data.table::fread(input = shareddataset,
header = TRUE)
taxonomy <- data.table::fread(input = taxonomydataset)
shared <- as.data.frame(shared)
desgroups <- shared$Group
shared.x <- shared[,4:ncol(shared)]
rownames(shared.x) <- desgroups
shared.t <- as.data.frame(t(shared.x)) # transpose: OTUs in rows, samples in columns
shared.t.ns <- shared.t[which(rowSums(shared.t)!=1),] # remove absolute singletons
sharedns <- data.frame(label=rep(0.03,ncol(shared.t.ns)),
                      Group=colnames(shared.t.ns),
                      numOtus=nrow(shared.t.ns),t(shared.t.ns))
taxonomy.spl <- CMETNGS::preformattax(taxonomy)
taxonomy.np <- taxonomy.spl %>% dplyr::select(-dplyr::contains("Prob"))
taxonomy.np.ns <- taxonomy.np[which(rownames(taxonomy.np) %in%
rownames(shared.t.ns)),]
barplot.genus <- makebargraphrawggplot2(tax=taxonomy.np.ns,shared=shared.t.ns,
topn=8,taxlevel="Genus",shared.abs=TRUE,
tax.prob=FALSE,samples="testsample",
plot=TRUE)