ReadsOTUsTaxa: Taxonomy analyses for multiple data sets

In walterxie/ComMA: Community Matrix Analysis

Description

Taxonomic summary of OTUs and reads for multiple data sets, and bar chart for visualization. "count.1" column is number of OTUs including singletons, "sum.1" is number of reads including singletons, "count.2" is OTUs excluding singletons, "sum.2" is reads excluding singletons.

Usage

getCountsSums(..., input.list = FALSE, taxa.rank = "phylum",
  group.rank = "kingdom")

plotTaxonomy(all.counts.sums, taxa.ref = ComMA::taxa.ref.PLOSONE.2015,
  exclude.singletons = 1, taxa.rank = "phylum", group.rank = "kingdom",
  count.unclassified = FALSE, gene.levels = c("16S", "18S", "26S", "ITS",
  "COI-300", "COI-650"), group.levels = c("ARCHAEA", "BACTERIA", "EUKARYOTA",
  "PROTOZOA", "CHROMISTA", "FUNGI", "PLANTAE", "ANIMALIA", "Unknown"),
  x.lab = "Phylum (or higher-level taxon)",
  y.lab = "Number of sequences or OTUs", legend.title = NULL,
  palette = NULL, title = "", title.size = 10, verbose = TRUE)

summReadsOTUsPipeline(cm.taxa.list, taxa.ref = ComMA::taxa.ref.PLOSONE.2015,
  taxa.rank = "phylum", group.rank = "kingdom", col.ranks = c("kingdom",
  "phylum", "class", "order"), gene.levels = c("16S", "18S", "26S", "ITS",
  "COI-300", "COI-650"), group.levels = c("ARCHAEA", "BACTERIA", "EUKARYOTA",
  "PROTOZOA", "CHROMISTA", "FUNGI", "PLANTAE", "ANIMALIA", "Unknown"), ...)

Arguments

...	Input of a list of community matrices, or comma separated multi-inputs.
input.list	Default to TRUE to unwrap list(...) to get the actual list if the input is a list of cm.
taxa.rank	The rank to display in the axis for counts of OTUs and reads.
group.rank	The rank to group taxa.rank to colour the figure.
all.counts.sums	The output produced by getCountsSums.
taxa.ref	The taxonomic reference data set to order taxonomic names nicely. But it removes the taxonomy not exsiting in the reference. Default to use a taxonomy reference data set taxa.ref.PLOSONE.2015 in the package. Set taxa.ref="", where length(taxa.ref) > 1, to plot all taxonomy.
exclude.singletons	If 0, then do not plot the number of sequences and OTUs excluding singleton OTUs. If 1, as default, just do not plot sequences excluding singleton. If 2, then plot all (including/excluding singleton).
count.unclassified	Count the taxonomy having 'unclassified' prefix, mostly in RDP classification, when using taxa.ref.PLOSONE.2015. The default is FALSE.
gene.levels	The level to order 'gene' column.
group.levels	The level to order 'gene' column.
x.lab, y.lab, title, title.size, legend.title, palette	See ggPlot.
cm.taxa.list	A list of cm.taxa merged by mergeCMTaxa. Require proper names of the list.
col.ranks	A vector or string of column name(s) of taxonomic ranks in the taxa table, detail to see mergeCMTaxa. Default to c("kingdom", "phylum", "class", "order").

Details

getCountsSums return a data frame concatenating counts of OTUs and reads given a list of data sets.

plotTaxonomy plots a circle-diamond graph of reads and OTUs coloured by taxonomic group and sumarised by getCountsSums.

Diamonds represent the number of sequences, open circles the number of OTUs including singleton OTUs, and filled circles the number of OTUs excluding singleton OTUs.

summReadsOTUsPipeline is a pipeline to summarise reads and OTUs by getCountsSums, and plot a circle-diamond graph by plotTaxonomy.

Examples

all.counts.sums <- ComMA::getCountsSums(cm.taxa.list, input.list=T, group.rank="kingdom", taxa.rank="phylum")

plotTaxonomy(all.counts.sums, taxa.ref=taxa.ref)

walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.